Thank you very much for your response.
I used pdb4amber before antechamber and the error didn't occur, there must be some problem in the input file. Anyway, as my protein has a calcium ion on the active site, I preferred to do it according to this tutorial I found
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm. I will post here if I have any problem.
Thank you!
Regards,
Thamires
<
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>
Building Bonded Model for A Ligand Binding Metalloprotein with MCPB.py - The Amber Molecular Dynamics Package<
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>
Newest version. The newest version of MCPB.py (version 3.0) has been released in AmberTools17, which is free of charge.And there is a binary distribution of serial ...
ambermd.org
________________________________
De: amber-request.ambermd.org <amber-request.ambermd.org>
Enviado: quarta-feira, 21 de julho de 2021 17:00
Para: amber.ambermd.org <amber.ambermd.org>
Assunto: AMBER Digest, Vol 3429, Issue 1
Send AMBER mailing list submissions to
amber.ambermd.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.ambermd.org/mailman/listinfo/amber
or, via email, send a message with subject or body 'help' to
amber-request.ambermd.org
You can reach the person managing the list at
amber-owner.ambermd.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of AMBER digest..."
AMBER Mailing List Digest
Today's Topics:
1. Re: tleap does not recognize inosine (Thamires Rocco Machado)
2. Re: tleap does not recognize inosine (Hector A. Baldoni)
3. Re: cudaMemcpy GpuBuffer ERROR (Ross Walker)
4. Re: tleap does not recognize inosine (David A Case)
5. Re: Gas phase Simulations (David A Case)
6. Re: 3D-RISM in amber20 (David A Case)
7. Re: Building Forcefield for Glycolipid Molecule (Razil Tahir)
8. Re: 3D-RISM in amber20 (tluchko)
9. Re: Building Forcefield for Glycolipid Molecule (Razil Tahir)
10. Re: Building Forcefield for Glycolipid Molecule (Razil Tahir)
11. Re: Gas phase Simulations (Kolattukudy P. Santo)
12. Re: Missing mtkpp directory after installation of
AmberTools21 (Pengfei Li)
13. Re: pc1 vs pc2 principal component analysis (Jenny 148)
14. Re: Building Forcefield for Glycolipid Molecule (Dr. Anselm Horn)
15. Re: Building Forcefield for Glycolipid Molecule (ABEL Stephane)
16. Re: Missing mtkpp directory after installation of
AmberTools21 (Anthony Nash)
17. Re: Gas phase Simulations (David A Case)
18. Displacement of coordinated Zn during the simulation
(Amit Sharma (Asstt. Prof., MCARS))
19. Re: Gas phase Simulations (Kolattukudy P. Santo)
----------------------------------------------------------------------
Message: 1
Date: Tue, 20 Jul 2021 21:42:46 +0000
From: Thamires Rocco Machado <thamiresroccomachado.hotmail.com>
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: Re: [AMBER] tleap does not recognize inosine
Message-ID:
<DM6PR19MB287390235C00BD8C5BBAC2F1CDE29.DM6PR19MB2873.namprd19.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Thank you very much for your response.
inosine is standalone as a nucleoside, so I will need to make my own parameters. Would you have any clue on how could I do it?
I tried with the antechamber too using gaff2, but it also failed to generate the force field.
Any help would be appreciated.
Thank you!
Regards,
Thamires
________________________________
De: amber-request.ambermd.org <amber-request.ambermd.org>
Enviado: ter?a-feira, 20 de julho de 2021 17:00
Para: amber.ambermd.org <amber.ambermd.org>
Assunto: AMBER Digest, Vol 3428, Issue 1
Send AMBER mailing list submissions to
amber.ambermd.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.ambermd.org/mailman/listinfo/amber
or, via email, send a message with subject or body 'help' to
amber-request.ambermd.org
You can reach the person managing the list at
amber-owner.ambermd.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of AMBER digest..."
AMBER Mailing List Digest
Today's Topics:
1. velocity trajectory output (Daniel Konstantinovsky)
2. adding counterions in cpptraj (Rohanizeidanlou, Sahar)
3. Re: The protonation state model of TYR in CpHMD (Adrian Roitberg)
4. Re: The protonation state model of TYR in CpHMD (He, Amy)
5. Re: velocity trajectory output (David A Case)
6. 3D-RISM in amber20 (Priya Dey)
7. Re: Where are the parameters for the SCREEN RADII section in
prmtop (Maximilian Ebert)
8. tleap does not recognize inosine (Thamires Rocco Machado)
9. MCPB.py 'OW' type error in AmberTools21 (David William Kastner)
10. Re: Missing mtkpp directory after installation of
AmberTools21 (Anthony Nash)
11. Re: Where are the parameters for the SCREEN RADII section in
prmtop (David A Case)
12. Re: tleap does not recognize inosine (David A Case)
13. Re: velocity trajectory output (Daniel Roe)
14. Re: adding counterions in cpptraj (Daniel Roe)
15. Re: tleap does not recognize inosine (Maria Nagan)
16. Re: Ligand clustering input .pdb file. (Daniel Roe)
17. Re: [cluster] Not all arguments handled: [ sil Sil avgout Avg
avgfmt restart ] (Daniel Roe)
18. Re: cudaMemcpy GpuBuffer ERROR (Gerardo Zerbetto De Palma)
19. Re: pc1 vs pc2 principal component analysis (Daniel Roe)
20. Gas phase Simulations (Kolattukudy P. Santo)
21. Re: adding counterions in cpptraj (Rohanizeidanlou, Sahar)
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Jul 2021 15:53:50 -0400
From: Daniel Konstantinovsky <daniel.konstantinovsky.yale.edu>
To: amber.ambermd.org
Subject: [AMBER] velocity trajectory output
Message-ID:
<CAGy_EAqpHy2yGSXJXBKwVrzWiKjrRq4g9z4RcJOnqVZxrfZ9Fw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi everyone,
I need accurate velocities to calculate correlation functions. I was
wondering if the velocities written by sander and pmemd take periodic
boundary conditions into account. For example, if a molecule jumps from one
end of the box to the other end because of PBC over an MD step, does the
corresponding velocity include the artifact of jumping across the box in
one step or is that excluded? In other words, does the velocity trajectory
include ridiculously large velocities due to wrapping? If yes, is there a
way to turn that off?
Thank you!
Daniel Konstantinovsky
------------------------------
Message: 2
Date: Mon, 19 Jul 2021 20:48:31 +0000
From: "Rohanizeidanlou, Sahar" <srohani3.calstatela.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] adding counterions in cpptraj
Message-ID:
<BYAPR06MB45658280A3CDF4386B2A917AE7E19.BYAPR06MB4565.namprd06.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello Amber Team,
Is there anyway to add counterions in cpptraj to make the net charge zero? I know tleap has good functions to accomplish this, but I was wondering if there's an easier way to do this in cpptraj directly.
Thanks for your support in advance.
Best regards,
Sahar
------------------------------
Message: 3
Date: Mon, 19 Jul 2021 17:26:44 -0400
From: Adrian Roitberg <roitberg.ufl.edu>
To: <amber.ambermd.org>
Subject: Re: [AMBER] The protonation state model of TYR in CpHMD
Message-ID: <702e6202-7366-1ff4-4492-e39c28eef9fc.ufl.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed
On 7/19/21 2:14 PM, He, Amy wrote:
> [External Email]
>
> Dear Amber Community,
>
>
> I have been doing constant pH MD simulations with Amber, and I have some questions about the protonation state model of the tyrosine residue.
>
> I noticed that the tyrosine residue has only two states: protonated and deprotonated. So I wonder how the position of the hydrogen atom HH (the phenyl group hydrogen) is determined, when the anionic tyrosine becomes protonated. According to the description of the protonation state models, a deprotonated residue would have a ?ghost? proton at the ionizable position.
>
> For the tyrosine residues, is this ?ghost? proton still counted in the bonded (bond, angle and torsional) potential and VDW interaction? If the SHAKE algorithm is used for the other hydrogens in the simulation, is the ?ghost? proton also constrained by SHAKE?
Hi
Is all of these cases, when we switch from protonated to unprotonated,
what happenes is that the proton one 'removes' is still there, as you
said, but its charge is zero and so is it vdw parameters.
Bond, angles, torsion s are all still being computed, but by turning off
electrostatics and vdw, those energies are not counted when trying to
change protonation state or when doing dynamics in the unprotonated state.
The proton, even as a ghost, still moves around and it can change
rotation. Once you protonate it again, it just stays where it is from
when it was a ghost, but now it acquires charge and vdw energies.
Is this ok ?
Adrian
>
> Thank you for your time and kind advice in advance!
>
>
> Thanks,
> Amy
>
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
> he.1768.osu.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIF-g&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=zQVy56ziuDUsraylQJQZdvBTb9dJyNdYv3MX8EY5N18&s=Q0k-vcAw_aCU0P-yiKDYHMnmS8J2YpyS8jTFY8hzDjg&e=
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
------------------------------
Message: 4
Date: Mon, 19 Jul 2021 22:02:45 +0000
From: "He, Amy" <he.1768.buckeyemail.osu.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] The protonation state model of TYR in CpHMD
Message-ID:
<CH0PR01MB7020D94E7E2AE070BA522842A3E19.CH0PR01MB7020.prod.exchangelabs.com>
Content-Type: text/plain; charset="Windows-1252"
Hi Dr. Roitberg,
Yes that is very clear and helpful! Thank you so much for your kind reply.
Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
From: Adrian Roitberg <roitberg.ufl.edu>
Date: Monday, July 19, 2021 at 5:29 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] The protonation state model of TYR in CpHMD
On 7/19/21 2:14 PM, He, Amy wrote:
> [External Email]
>
> Dear Amber Community,
>
>
> I have been doing constant pH MD simulations with Amber, and I have some questions about the protonation state model of the tyrosine residue.
>
> I noticed that the tyrosine residue has only two states: protonated and deprotonated. So I wonder how the position of the hydrogen atom HH (the phenyl group hydrogen) is determined, when the anionic tyrosine becomes protonated. According to the description of the protonation state models, a deprotonated residue would have a ?ghost? proton at the ionizable position.
>
> For the tyrosine residues, is this ?ghost? proton still counted in the bonded (bond, angle and torsional) potential and VDW interaction? If the SHAKE algorithm is used for the other hydrogens in the simulation, is the ?ghost? proton also constrained by SHAKE?
Hi
Is all of these cases, when we switch from protonated to unprotonated,
what happenes is that the proton one 'removes' is still there, as you
said, but its charge is zero and so is it vdw parameters.
Bond, angles, torsion s are all still being computed, but by turning off
electrostatics and vdw, those energies are not counted when trying to
change protonation state or when doing dynamics in the unprotonated state.
The proton, even as a ghost, still moves around and it can change
rotation. Once you protonate it again, it just stays where it is from
when it was a ghost, but now it acquires charge and vdw energies.
Is this ok ?
Adrian
>
> Thank you for your time and kind advice in advance!
>
>
> Thanks,
> Amy
>
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
> he.1768.osu.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIF-g&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=zQVy56ziuDUsraylQJQZdvBTb9dJyNdYv3MX8EY5N18&s=Q0k-vcAw_aCU0P-yiKDYHMnmS8J2YpyS8jTFY8hzDjg&e=
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!gK0fjvncoJ9B3JQdfEeRYARnlxtWw1MfP0i7yRLBr9nQq0UfpUMdXSHDh4cA9c7mVeD-XjquEKE$<
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------------------------------
Message: 5
Date: Mon, 19 Jul 2021 21:25:16 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] velocity trajectory output
Message-ID:
<20210720012516.s3n6dx3qno6nrfod.ipo3912l119.rad.rutgers.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Mon, Jul 19, 2021, Daniel Konstantinovsky wrote:
>
>I need accurate velocities to calculate correlation functions. I was
>wondering if the velocities written by sander and pmemd take periodic
>boundary conditions into account. For example, if a molecule jumps from one
>end of the box to the other end because of PBC over an MD step, does the
>corresponding velocity include the artifact of jumping across the box in
>one step or is that excluded? In other words, does the velocity trajectory
>include ridiculously large velocities due to wrapping? If yes, is there a
>way to turn that off?
Wrapping is off by default. You have to turn it "on" by setting iwrap=1, but
that should be necessary only in a very few situations. We recommend the
defaults, which use netcdf format for trajectories and restart files, and
leaving iwrap=0. (If you later need to do some imaging for visualization
pruposes, use the command in cpptraj for that purpose.)
That said, I don't think you will get odd velocities if you do set iwrap=1.
But you could run a test to make sure.
...dac
------------------------------
Message: 6
Date: Tue, 20 Jul 2021 12:05:08 +0530
From: Priya Dey <mmv.priya.dey.gmail.com>
To: amber.ambermd.org
Subject: [AMBER] 3D-RISM in amber20
Message-ID:
<CAFK7kO=sxFviaAXVTeoe1Y_LvqHjY1iv6NMZBvvCvn+d9f3QQg.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Initially, we were using amber 12 for 3D-RISM calculation using
*rism3d.snglpnt.MPI
command*.
Then, we have updated the amber12 software to amber20. We have tried to run
the following script for 3d rism calculation-
*rism3d.snglpnt.MPI --pdb pdbname --prmtop parameterfie --closure kh
--buffer -1 --solvcut 32 --verbose 2 --xvv SPC-1D.xvv --solvbox
128,128,128 --ng 256,256,256 --grdspc 0.5,0.5,0.5 > logfile*
the SPC-1d.xvv file is generated using 1D RISM.
The following error is coming: *ERROR: a RESTART or TRAJ file is required*
*In the amber20 manual, it is written the required inputs are "pdb file,
prmtop file and xvv file". *
So my query is (a) why is this error coming?
(b) If a restart file has to be used, which restart file should I use? (as
I have tried with the initial restart file that is generated during system
preparation: in that case the system is reading coordinates from the
restart file whatever the pdb is given, and the output is similar for
different pdbs.)
(c) If a traj file has to be used, which traj file should I use?
*Priya Dey*
*Research Scholar*
*c/o Prof. Parbati Biswas*
*Department of Chemistry *
*University of Delhi*
*Delhi,110007*
*India*
*Contact Number-8010903736*
------------------------------
Message: 7
Date: Tue, 20 Jul 2021 08:21:33 -0400
From: Maximilian Ebert <max.ebert.me.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Where are the parameters for the SCREEN RADII
section in prmtop
Message-ID: <0F2DE601-BD9B-489B-AA9E-88276358341A.me.com>
Content-Type: text/plain; charset=utf-8
I have my own prmtop write to create an input forcefield to pmemd. I could find all the necessary information to parameterize the protein / ligand from the forcefield files provided in the dat folder of the amber installation. The only section I can?t write is the RADII and SCREEN section to fully support all GB modes. I would like to know where tleap looks to write this section. Where do these numbers come from? Which parameter files are read to fill the section with the appropriate values for the corresponding atom types. We cannot depend on the amber tools and hence are trying to write a fully compliant prmtop file.
In the source code you gave me I couldn?t find any SCREEN value 0.79, 0.72 or 0.85. So I am still puzzled how tleap gets these exact numbers.
> On Jul 19, 2021, at 8:14 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> I'm not understanding the problem, the radii are listed in the text you
> quoted. Different parameters may be in different places, for example the
> radii are in the prmtop (these are chosen in theeap input, they are not
> specific to a certain gb model) and the screening parameters are in the
> source code that I gave before.
>
> On Mon, Jul 19, 2021, 8:07 AM Maximilian Ebert <max.ebert.me.com> wrote:
>
>> Thanks for the answer. I looked at the file but I can?t find the numbers I
>> see for Alanine in the prmtop when created via tleap:
>>
>> ?.
>> 0
>> %FLAG RADIUS_SET
>>
>> %FORMAT(1a80)
>>
>> modified Bondi radii (mbondi)
>>
>> %FLAG RADII
>>
>> %FORMAT(5E16.8)
>>
>> 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
>> 1.70000000E+00
>> 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
>> 1.50000000E+00
>> 1.50000000E+00
>> %FLAG SCREEN
>>
>> %FORMAT(5E16.8)
>>
>> 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
>> 7.20000000E-01
>> 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
>> 8.50000000E-01
>> 8.50000000E-01
>> %FLAG IPOL
>>
>> %FORMAT(1I8)
>>
>> 0
>> ?
>>
>> What am I missing? I found the constants alpha, beta, etc. but not the
>> values for SCREEN + RADII necessary for OBC GB.
>>
>> Thanks
>>
>>> On Jul 13, 2021, at 4:27 PM, Carlos Simmerling <
>> carlos.simmerling.gmail.com> wrote:
>>>
>>> look at mdin_ctrl_dat.F90 in src/pmemd/src.
>>> they are also written to the mdout file at the beginning of the run.
>>>
>>>
>>> On Tue, Jul 13, 2021 at 2:27 PM Maximilian Ebert <max.ebert.me.com>
>> wrote:
>>>
>>>> Thanks, but is there any text file with the parameters or do they exist
>>>> only within the parmed code?
>>>>
>>>>> On Jul 7, 2021, at 4:26 PM, David A Case <david.case.rutgers.edu>
>> wrote:
>>>>>
>>>>> On Wed, Jul 07, 2021, Maximilian Ebert wrote:
>>>>>
>>>>>> For GB in AMBER the screen/radii section in prmtop files is necessary
>> in
>>>>>> some modes. Where do I find the parameters in $AMBERHOME/dat to put
>> into
>>>>>> these sections? I simply can?t find the origin of the data if the
>>>> general
>>>>>> born screening parameters.
>>>>>
>>>>> You can get these by using the "changeRadii" command in parmed.
>>>>>
>>>>> ...good luck...dac
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 8
Date: Tue, 20 Jul 2021 14:12:54 +0000
From: Thamires Rocco Machado <Thamiresroccomachado.hotmail.com>
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: [AMBER] tleap does not recognize inosine
Message-ID:
<DM6PR19MB28739DF3ACA504725EDD906FCDE29.DM6PR19MB2873.namprd19.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear all amber users,
I'm studying a protein that has inosine as its substrate. I'm not getting amber to recognize inosine when I load the PDB file into tleap. I researched that amber has parameters for inosine, but I don't know how it recognizes the pdb.
The PDB I'm using is:
HETATM 1 C5' I 4 1 -13.592 13.948 17.001 0.00 0.00 C
HETATM 2 O5' I 4 1 -13.689 12.651 16.407 0.00 0.00 O
HETATM 3 C4' I 4 1 -13.720 15.139 16.027 0.00 0.00 C
HETATM 4 O4' I 4 1 -14.771 15.096 15.029 0.00 0.00 O
HETATM 5 C3' I 4 1 -14.043 16.386 16.848 0.00 0.00 C
HETATM 6 O3' I 4 1 -13.022 17.386 16.620 0.00 0.00 O
HETATM 7 C2' I 4 1 -15.490 16.785 16.468 0.00 0.00 C
HETATM 8 O2' I 4 1 -15.638 18.117 15.969 0.00 0.00 O
HETATM 9 C1' I 4 1 -15.990 15.789 15.420 0.00 0.00 C
HETATM 10 N1 I 4 1 -17.652 10.941 14.883 0.00 0.00 N
HETATM 11 C2 I 4 1 -17.055 11.743 13.979 0.00 0.00 C
HETATM 12 N3 I 4 1 -16.701 13.008 14.258 0.00 0.00 N
HETATM 13 C4 I 4 1 -16.937 13.538 15.500 0.00 0.00 C
HETATM 14 C5 I 4 1 -17.584 12.725 16.530 0.00 0.00 C
HETATM 15 C6 I 4 1 -17.936 11.351 16.132 0.00 0.00 C
HETATM 16 O6 I 4 1 -18.484 10.615 16.972 0.00 0.00 O
HETATM 17 N7 I 4 1 -17.700 13.473 17.637 0.00 0.00 N
HETATM 18 C8 I 4 1 -17.161 14.672 17.360 0.00 0.00 C
HETATM 19 N9 I 4 1 -16.730 14.709 16.084 0.00 0.00 N
END
Thanks,
Thamires
------------------------------
Message: 9
Date: Tue, 20 Jul 2021 14:51:12 +0000
From: David William Kastner <kastner.mit.edu>
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: [AMBER] MCPB.py 'OW' type error in AmberTools21
Message-ID: <01EC26BF-641D-4314-BF07-1982F98C8281.mit.edu>
Content-Type: text/plain; charset="utf-8"
Hi everyone!
When performing the MCPB step ?MCPB.py -i 1OS7.in -s 2?, I get the following error:
Traceback (most recent call last):
File "/home/kastner/packages/miniconda3/envs/AmberTools21/bin/MCPB.py", line 665, in <module>
gene_pre_frcmod_file(ionids, premol2fs, stpdbf, stfpf, smresf, prefcdf,
File "/home/kastner/packages/miniconda3/envs/AmberTools21/lib/python3.9/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py", line 132, in gene_pre_frcmod_file
print('YES', atyp2 + massparms[atyp1], file=fmf)
KeyError: 'OW'
My system is the hydroxylase TauD and I am exploring a conformation where there are waters coordinated to the Fe metal center. I am performing the calculation with AmberTools21 and g16. I have read over all similar posts and have ruled out common errors that can cause this such as assigning the wrong ?ion_ids? to the metal and incorrect atom types. I also reran the calculation with g09 but saw the same behavior. I am following the tutorial exactly and have successfully used MCPB many times before but have never encountered this error. Interestingly, if I use an older version such as AmberTools16, it does not throw this KeyError: 'OW' error for the oxygen in the water molecule coordinated to the metal. Any help would be much appreciated! I can also share the directory if anyone has seen a similar error.
Thank you,
David
---
David Kastner
Ph.D. student | Bioengineering
MIT | Tidor & Kulik Labs
kastner.io
------------------------------
Message: 10
Date: Tue, 20 Jul 2021 14:55:59 +0000
From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: Re: [AMBER] Missing mtkpp directory after installation of
AmberTools21
Message-ID:
<LO2P265MB26079BEE84D287EF27DCD5A389E29.LO2P265MB2607.GBRP265.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="us-ascii"
In answer to my own question, I created a new environment and I've downloaded and installed AmberTools21 from source.
However, having now looked through the manual pdf, and compared it to the HTML page dating 2015 which begins with running genMetalFF.sh, all of the required variables for MCPB.py aren't in the bcl files that genMetalFF originally generated.
Rather than hack around hoping something will work, is there a latest and greater bonded model tutorial specifically designed with the latest MCPB.py in mind?
Thanks
Anthony
Kind regards
Dr Anthony Nash PhD MRSC
Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/
________________________________
From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
Sent: 19 July 2021 14:37
To: amber.ambermd.org <amber.ambermd.org>
Subject: Missing mtkpp directory after installation of AmberTools21
Dear all,
I'm a new user of AMBER but a long time MD modeller and I'm hoping I can get some help resolving a post-installation concern over what and where some of the files are.
I am trying to step through the bonded metal-binding centre tutorials given here: https://ambermd.org/tutorials/advanced/tutorial20/mcpb.php
The only difference is that I'm using my own set of pdb files. Six in total; two zinc-based and four calcium-based coordination centres.
I installed AmberTools21 in Linux (in fact, it was WSL2 Ubuntu) using conda. The installation didn't flag up any problems.
These are my concerns/issues:
Firstly, as per the tutorial linked above, I wasn't able to find genMetalFF.sh in my AMBERHOME directory structure. So, I downloaded the file from the link provided in the tutorial and generated the corresponding setup files for MCPB.
Then, the next slight concern I ran into was upon investigating zinc_1201_settings.bcl (one of my generated files) I noticed the directory structure AMBERHOME/dat/mtkpp/ is missing!
Finally, before resorting to this email, I was unable to find the MCPB executable. Instead, I'm able to find MCPB.py (of which, I've noticed the command line arguments are slightly different to the command line arguments of MCP B). Either way, I decided to execute the python executable and I got the following error:
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/AmberTools21/bin/MCPB.py", line 67, in <module>
options.step = options.step.lower()
AttributeError: 'NoneType' object has no attribute 'lower'
All suggestions are welcome.
Many thanks
Anthony
------------------------------
Message: 11
Date: Tue, 20 Jul 2021 11:03:51 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Where are the parameters for the SCREEN RADII
section in prmtop
Message-ID:
<20210720150351.3vb65l73xi7bxq36.n7227-owl117c01.rad.rutgers.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On Tue, Jul 20, 2021, Maximilian Ebert wrote:
>I have my own prmtop write to create an input forcefield to pmemd. I
>could find all the necessary information to parameterize the protein /
>ligand from the forcefield files provided in the dat folder of the amber
>installation. The only section I can?t write is the RADII and SCREEN
>section to fully support all GB modes. I would like to know where tleap
>looks to write this section. Where do these numbers come from? Which
>parameter files are read to fill the section with the appropriate values
>for the corresponding atom types. We cannot depend on the amber tools and
>hence are trying to write a fully compliant prmtop file.
Look in amber20_src/AmberTools/src/parmed/parmed/tools/changeraii.py.
That has python code for assigning radii and screening parameters. You
should be able to adapt this to your codes.
....good luck...dac
------------------------------
Message: 12
Date: Tue, 20 Jul 2021 11:10:56 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tleap does not recognize inosine
Message-ID:
<20210720151056.xyr3eca35jvhhs7a.n7227-owl117c01.rad.rutgers.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Tue, Jul 20, 2021, Thamires Rocco Machado wrote:
>
>I'm studying a protein that has inosine as its substrate. I'm not getting
>amber to recognize inosine when I load the PDB file into tleap. I
>researched that amber has parameters for inosine,
I don't know that inosine is in any standard library. You might look
closely at the research you did, to find more details. Further, "inosine"
as a protein substrate is probably chemically different from the nucleotide
"inosine" that might be incorporated into a nucleic acid. (e.g. your pdb
file looks like a nucleoside.
It is likely that you can just feed your ligand to antechamber to get GAFF2
parameters. It's also worth doing a search on "inosine Amber", if you've
not already done that.
Some one on the list might also chime in with some more detailed help.
....dac
------------------------------
Message: 13
Date: Tue, 20 Jul 2021 11:41:06 -0400
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] velocity trajectory output
Message-ID:
<CAAC0qOYRPuGmkRUb_h9eGYnXJ-fD0mJPCqt=KxCjRJ=tXGXyrA.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
On Mon, Jul 19, 2021 at 3:54 PM Daniel Konstantinovsky
<daniel.konstantinovsky.yale.edu> wrote:
> I need accurate velocities to calculate correlation functions. I was
> wondering if the velocities written by sander and pmemd take periodic
> boundary conditions into account. For example, if a molecule jumps from one
> end of the box to the other end because of PBC over an MD step, does the
> corresponding velocity include the artifact of jumping across the box in
> one step or is that excluded? In other words, does the velocity trajectory
> include ridiculously large velocities due to wrapping? If yes, is there a
No. Coordinate wrapping (from iwrap=1) only affects the coordinates
that are written to trajectory/restart files. Internally, the
coordinates are not modified. So iwrap does not affect velocities (or
forces). If you see otherwise, definitely let us know, that would be a
bug.
-Dan
> way to turn that off?
>
> Thank you!
> Daniel Konstantinovsky
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 14
Date: Tue, 20 Jul 2021 11:43:40 -0400
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] adding counterions in cpptraj
Message-ID:
<CAAC0qOZrntwUad+m6gJRtrN4epd1Eo55KCLsuN+tDxAjYzmZow.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
No. While there are some commands that are related to modifying
systems, Cpptraj is really just for trajectory processing/data
analysis. I think if I started adding general system preparation
commands I'd be asking for a lot of trouble :-). Not that I haven't
been tempted at times...
-Dan
On Mon, Jul 19, 2021 at 4:48 PM Rohanizeidanlou, Sahar
<srohani3.calstatela.edu> wrote:
>
> Hello Amber Team,
>
> Is there anyway to add counterions in cpptraj to make the net charge zero? I know tleap has good functions to accomplish this, but I was wondering if there's an easier way to do this in cpptraj directly.
>
> Thanks for your support in advance.
>
> Best regards,
> Sahar
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 15
Date: Tue, 20 Jul 2021 11:51:30 -0400
From: Maria Nagan <maria.c.nagan.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tleap does not recognize inosine
Message-ID: <31B6F7F3-A649-40C5-8BEB-E5D7B3F64C1F.gmail.com>
Content-Type: text/plain; charset=us-ascii
Dear Thamires,
You need both an lib file and frcmod parameters. If it is standalone inosine as a nucleoside, you will need to make your own parameters.
For just the inosine base charges in a nucleotide:
I have ESP charges for inosine in RNA.
https://pubs.acs.org/doi/full/10.1021/ja9842565 <
https://pubs.acs.org/doi/full/10.1021/ja9842565>
As well, SantaLucia and Schlegel have RESP charges for the base,
all_modrna08.lib and all_modrna08.frcmod
https://pubs.acs.org/doi/abs/10.1021/ct600329w <
https://pubs.acs.org/doi/abs/10.1021/ct600329w>
Maria
> On Jul 20, 2021, at 11:10 AM, David A Case <dacase.chem.rutgers.edu> wrote:
>
> On Tue, Jul 20, 2021, Thamires Rocco Machado wrote:
>>
>> I'm studying a protein that has inosine as its substrate. I'm not getting
>> amber to recognize inosine when I load the PDB file into tleap. I
>> researched that amber has parameters for inosine,
>
> I don't know that inosine is in any standard library. You might look
> closely at the research you did, to find more details. Further, "inosine"
> as a protein substrate is probably chemically different from the nucleotide "inosine" that might be incorporated into a nucleic acid. (e.g. your pdb
> file looks like a nucleoside.
>
> It is likely that you can just feed your ligand to antechamber to get GAFF2
> parameters. It's also worth doing a search on "inosine Amber", if you've
> not already done that.
>
> Some one on the list might also chime in with some more detailed help.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 16
Date: Tue, 20 Jul 2021 12:06:44 -0400
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Ligand clustering input .pdb file.
Message-ID:
<CAAC0qObb1w0N2qTPy1cNZfbJny__7ZaDCVz-EFZwBmr5kZ0-xQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
On Mon, Jul 19, 2021 at 5:14 AM Samuele Di Cristofano
<samueledicristofano95.gmail.com> wrote:
>
> The problem is that only few of my output files ( .pdb of representative
> clusters members) exhibits wrong connectivity when visualized.
The PDB format doesn't store topology information, so most programs
(including cpptraj, VMD, etc) have to try and guess at how things are
bonded. Depending on the structure, those guesses are not always
correct. You would be better off using a format that has actual
topology information (i.e. mol2, amber topology, psf, etc) when
clustering/visualizing the output. In fact, I recommend that you write
out mol2 files instead of PDBs from your clustering so you can see
exactly what cpptraj thinks the PDB topology is.
-Dan
> This doesn't happen when I use only 20 models (i.e. output from a single
> docking run) as input.
>
> Could someone help me to figure out where the problem is?
> The 'trajin' command needs a particular .pdb format ?
>
> Thanks in advance.
> Samuele
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 17
Date: Tue, 20 Jul 2021 12:12:44 -0400
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil
avgout Avg avgfmt restart ]
Message-ID:
<CAAC0qOZZkUjwkKFtRXira_6LDXMvUaHGyzOijy_w7PvYV=ZhNg.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
On Sat, Jul 17, 2021 at 4:01 AM ??? <
1915391047.st.gxu.edu.cn> wrote:
>
> Hello Daniel,
> Thank you for your suggestion! Your suggestion worked perfectly. I am using CPPTRAJ: Trajectory Analysis. V14.25Is the version too much low?
Yes - that version is before the cluster silhouette calculation was
introduced (also it's about 7 years old!). I always recommend using
the latest version from either AmberTools or direct from GitHub:
https://github.com/Amber-MD/cpptraj
Note that when cpptraj started being developed primarily on GitHub, I
moved from the old AmberTools versioning scheme with 2 numbers
(<AmberToolsVersion>.<patch>) to an internal versioning scheme with 3
numbers (<major>.<minor>.<revision>). So the more recent versions of
cpptraj are numbered <major>.<minor>.<revision>.
-Dan
My intent is using cluster to find the lowest energy structure
according the distance data calculated from reweighting analysis.
> According to your suggestion and another friend Victor?I am using the cpptraj version V18.01 and modified the input to :parm nanobody.prmtop
> trajin 06_gamd_3.mdcrdcluster c1 \hieragglo epsilon 3.0 clusters 10 averagelinkage \rms :111.OG1,:113.H,:108.O,:111.H \sieve 10 random \out cnumvtime.dat \sil sil \summary summary.dat \info info.dat \cpopvtime cpopvtime.agr normframe \repout rep repfmt pdb \singlerepout singlerep.nc singlerepfmt netcdf \avgout avg avgfmt restart
>
> It can calculate normally ?Thank you very much ! Have a nice weekend!
> Best wishes.
> Hongyan Yu
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ????Daniel Roe <daniel.r.roe.gmail.com>
> ?????2021-07-15 23:48:17
> ????AMBER Mailing List <amber.ambermd.org>
> ???Re: [AMBER] [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ]>Hi,
> >
> >What version of cpptraj are you using (i.e. what is the output of
> >'cpptraj --version')?
> >
> >-Dan
> >
> >On Thu, Jul 15, 2021 at 3:03 AM ??? <1915391047.st.gxu.edu.cn> wrote:
> >>
> >> Dear Amber users,
> >>
> >>
> >> I am trying to run cpptraj for cluster analysis
> >>
> >>
> >>
> >> Script that I am following is
> >>
> >>
> >> parm nanobody.prmtop
> >> trajin 06_gamd_3.mdcrd
> >> cluster c1 \
> >> hieragglo epsilon 3.0 clusters 10 \
> >> averagelinkage \
> >> rms :111.OG1,:113.H \
> >> sieve 10 random \
> >> out cnumvtime.dat \
> >> sil Sil \
> >> summary summary.dat \
> >> info info.dat \
> >> cpopvtime cpopvtime.agr normframe \
> >> repout rep repfmt pdb \
> >> singlerepout singlerep.nc singlerepfmt netcdf \
> >> avgout Avg avgfmt restart
> >>
> >>
> >>
> >> All the time I am getting an error
> >>
> >>
> >> Error: [cluster] Not all arguments handled: [ sil Sil avgout Avg avgfmt restart ]
> >>
> >>
> >> When I keep the process running ?it can output nine structure but during the process will appear warning
> >>
> >> Too many iterations in routine! Convergence failed
> >>
> >>
> >>
> >> I don't know how to deal with this error. Please help me!
> >>
> >>
> >> Your kind help will be highly appreciated!
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 18
Date: Tue, 20 Jul 2021 13:15:51 -0300
From: Gerardo Zerbetto De Palma <g.zerbetto.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cudaMemcpy GpuBuffer ERROR
Message-ID:
<CAOMpsaXJ7xTMrieVZ=GhxyB+GZkYg2HKwYBx7+gPSBT65iHe=A.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Plot twist & update:
We managed to perform the GPU swap and, for now, it appears that the
problem is the power supply. The TITAN V GPU is now in a computer with
better (80+ bronze) power supply and has been running during the last 24
hours without any kind of problem. On the contrary, the RTX2080 GPU that is
now in the former TITAN V computer, has crashed after running for 12 hours.
Remarkably, no cudaMemcpy error appeared in the output, but it seemed that
the hard drive could't be accessed at all. We are going to run some
additional tests just to confirm this, but it is clear that the problem is
not in the code nor the GPU nor the simulated system.
Thank you all for all the help!
Regards
Gera!
El lun, 19 jul 2021 a las 12:13, Gerardo Zerbetto De Palma (<
g.zerbetto.gmail.com>) escribi?:
> We tried older simulations that we had run on GTX1080 and RTX2080 and they
> all show the same problem. Another remarkable thing is that we had run
> similar simulations in the TITAN V without any trouble, and this type of
> crash started to appear more often. Additionally, when the sim crashes,
> also the whole computer crashes and we have to force reboot it. That is why
> we will try to swap the GPUs.
> Thanks a lot, Carlos!?
> Regards
>
> El lun, 19 jul 2021 a las 12:04, Carlos Simmerling (<
> carlos.simmerling.gmail.com>) escribi?:
>
>> that's interesting that it sounds like it is the GPU and not the system
>> setup itself. Do other simulations of similar size work ok on the Titan V?
>>
>> On Mon, Jul 19, 2021 at 11:00 AM Gerardo Zerbetto De Palma <
>> g.zerbetto.gmail.com> wrote:
>>
>> > Hi Carlos. Thanks for the help. The system we are trying to simulate is
>> a
>> > nPT membrane embedded protein tetramer. We are just running a plain MD
>> sim,
>> > so no additional parameters are set. The initial coordinates were
>> obtained
>> > from a previous simulation that we had run with the same parameters, so
>> > those coordinates are from a very well thermalized system. We just made
>> a
>> > single point mutation and made a minimization just to relax any
>> clashes. It
>> > is quite remarkable that the same system is being simulated in an
>> RTX2080
>> > (in another computer) without any trouble but when we run it in the
>> TITAN V
>> > it randomly crashes. Now we will try swapping the GPUs just to discard
>> that
>> > it is not a problem with any other computer component.
>> > Thanks a lot, again.
>> > Regards
>> >
>> > The original post was this one:
>> > *Hi everyone.*
>> > *We were trying to run some simulations of a membrane protein on an
>> NVIDIA
>> > TITAN V and got stuck by some cudaMemcpy that came in different
>> flavors:*
>> >
>> >
>> >
>> > *cudaMemcpy GpuBuffer::Upload failed unspecified launch
>> failurecudaMemcpy
>> > GpuBuffer::Download failed unspecified launch failure*
>> >
>> > *cudaMemcpy GpuBuffer::Download failed an illegal instruction was
>> > encountered*
>> >
>> > *Firstly we started running the sim using amber 18, restarting the sim
>> > every 5 nanoseconds to get consecutive 5ns trajectories. After
>> simulating
>> > 25 nanoseconds, the program stopped randomly. Then we tried to repeat
>> the
>> > simulation that had failed (using the same random seed and initial
>> > coordinates) and the simulation succeeded, but the same error came up
>> in a
>> > subsequent simulation. These errors kept coming at a random timestep
>> when
>> > we restarted the simulations. Energies in the output seemed to be OK and
>> > simulations sometimes proceeded without errors when restarted. Hoping
>> that
>> > this was a bug, we compiled amber 20 and ran the same simulations and
>> had
>> > the same random cudaMemcpy errors. Just to check if the simulated system
>> > was fine, we are also running it in a RTX2080 with amber 18 without
>> > problems, so far.*
>> >
>> > *We are running out of ideas here so here we are reaching out to the
>> > community for some help in this matter. We will appreciate every idea or
>> > question that can enlighten us to solve this puzzle.*
>> >
>> > El lun, 19 jul 2021 a las 11:08, Carlos Simmerling (<
>> > carlos.simmerling.gmail.com>) escribi?:
>> >
>> > > for ff19SB problems, make sure your Amber version is completely
>> updated
>> > > with current patches. There was a fix a while back that corrected an
>> > error
>> > > that could lead to failures with some force fields including ff19SB.
>> > > Information on applying patches is found here:
>> > > http://ambermd.org/AmberPatches.php
>> > >
>> > > for the problem with ff14SB, I did not see the original post. More
>> > details
>> > > would be helpful, especially about the system you are simulating (is
>> it
>> > > only protein, or more? did you use any other parameters except ff14SB?
>> > > Where were the initial coordinates obtained?).
>> > >
>> > >
>> > >
>> > >
>> > > On Mon, Jul 19, 2021 at 9:46 AM Gerardo Zerbetto De Palma <
>> > > g.zerbetto.gmail.com> wrote:
>> > >
>> > > > Hi we are using ff14SB forcefield and the errors still appear.
>> > > > Thanks for the help!
>> > > > Regards
>> > > >
>> > > > Gerardo Zerbetto
>> > > >
>> > > > <
>> > > >
>> > >
>> >
>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> > > > >
>> > > > Virus-free.
>> > > > www.avg.com<http://www.avg.com>
>> > > > <
>> > > >
>> > >
>> >
>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> > > > >
>> > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>> > > >
>> > > > El vie, 16 jul 2021 a las 18:29, Rafa? Madaj (<rmadaj.cbmm.lodz.pl
>> >)
>> > > > escribi?:
>> > > >
>> > > > > Hi,
>> > > > >
>> > > > > Which force field are you using? I had exactly same problem with
>> > > ff19SB.
>> > > > > After changing into ff14SB the problem disappeared.
>> > > > >
>> > > > > Regards,
>> > > > >
>> > > > > Rafal
>> > > > >
>> > > > > On 16.07.2021 18:01, Gerardo Zerbetto De Palma wrote:
>> > > > > > Hi everyone.
>> > > > > > We were trying to run some simulations of a membrane protein on
>> an
>> > > > NVIDIA
>> > > > > > TITAN V and got stuck by some cudaMemcpy that came in different
>> > > > flavors:
>> > > > > >
>> > > > > > cudaMemcpy GpuBuffer::Upload failed unspecified launch failure
>> > > > > > cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>> > > > > > cudaMemcpy GpuBuffer::Download failed an illegal instruction was
>> > > > > encountered
>> > > > > >
>> > > > > > Firstly we started running the sim using amber 18, restarting
>> the
>> > sim
>> > > > > every
>> > > > > > 5 nanoseconds to get consecutive 5ns trajectories. After
>> simulating
>> > > 25
>> > > > > > nanoseconds, the program stopped randomly. Then we tried to
>> repeat
>> > > the
>> > > > > > simulation that had failed (using the same random seed and
>> initial
>> > > > > > coordinates) and the simulation succeeded, but the same error
>> came
>> > up
>> > > > in
>> > > > > a
>> > > > > > subsequent simulation. These errors kept coming at a random
>> > timestep
>> > > > when
>> > > > > > we restarted the simulations. Energies in the output seemed to
>> be
>> > OK
>> > > > and
>> > > > > > simulations sometimes proceeded without errors when restarted.
>> > Hoping
>> > > > > that
>> > > > > > this was a bug, we compiled amber 20 and ran the same
>> simulations
>> > and
>> > > > had
>> > > > > > the same random cudaMemcpy errors. Just to check if the
>> simulated
>> > > > system
>> > > > > > was fine, we are also running it in a RTX2080 with amber 18
>> without
>> > > > > > problems, so far.
>> > > > > >
>> > > > > > We are running out of ideas here so here we are reaching out to
>> the
>> > > > > > community for some help in this matter. We will appreciate every
>> > idea
>> > > > or
>> > > > > > question that can enlighten us to solve this puzzle.
>> > > > > >
>> > > > > > Regards!
>> > > > > > Gerardo Zerbetto De Palma
>> > > > > >
>> > > > > > <
>> > > > >
>> > > >
>> > >
>> >
>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> > > > > >
>> > > > > > Virus-free.
>> > > > > > www.avg.com<http://www.avg.com>
>> > > > > > <
>> > > > >
>> > > >
>> > >
>> >
>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>> > > > > >
>> > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>> > > > > > _______________________________________________
>> > > > > > AMBER mailing list
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>> > > > >
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
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>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
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>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
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>
------------------------------
Message: 19
Date: Tue, 20 Jul 2021 14:10:40 -0400
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] pc1 vs pc2 principal component analysis
Message-ID:
<CAAC0qObaouLA+PyKmQjLGXA1WftLCA2NcDpaX4Jt9XRDrGX-MQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
On Fri, Jul 16, 2021 at 3:43 PM Jenny 148 <jenny.rs140.gmail.com> wrote:
> I am working with a protein system. I have constructed the
> diagonalized coordinate covariance matrix for eigenmodes in a file
> evectors.dat with the command line being beg 1 end 20 (though I had only 11
> columns, the reason of which I am not sure. After that using the following
It's not clear what you mean here - which file had 11 columns? Can you
post the exact input you are using, and point out the file that you
unsure about that has 11 columns?
> readdata evectors.dat name Modes
> # Now create separate PC projections for each trajectory
> projection A1 modes Modes out pca12-ca beg 1 end 2 :1-831.CA
>
> After which I get a file pca12-ca, which looked somewhat like this:
> #Frame Mode1 Mode2
> 1 36.824 5.205
> 2 35.917 5.359
> 3 34.797 6.404
> 4 34.637 8.611
> 5 35.224 9.040
> ...........(Blanking out the rest)
>
> My query is whether the pca12-ca file which I got, the actual PC1 vs PC2
> file? I mean, would plotting the 2nd and 3rd column in the above file as X
> and Y axis, allow me to get a scatter plot between the First and second
Yes. You are projecting the coordinates of CA atoms of residues 1-831
on the eigenvectors read in from evectors.dat (presumably generated
from the same coordinate selection), only for eigenvectors (modes) 1
and 2.
Hope this helps,
-Dan
> principal component of my trajectory?
>
> --
> Jenny R.S
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 20
Date: Tue, 20 Jul 2021 14:17:32 -0400
From: "Kolattukudy P. Santo" <santotheophys.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Gas phase Simulations
Message-ID:
<CAAoy1or0bKummCeaAPsUrmBAXAd9qQXCMtPmsja4Rk7Dgcf-KQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hello all.
Is it useful to use ntp=1, ie pressure coupling, in gas phase simulations
for polymer ( that is without solvent) in the equilibration stage like in
http://ambermd.org/tutorials/advanced/tutorial27/pet.htm ?
Does that make any change over an NVT simulation at the same conditions ?
Santo
--
Best Regards
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
---------------------------------------------------------
------------------------------
Message: 21
Date: Tue, 20 Jul 2021 18:57:07 +0000
From: "Rohanizeidanlou, Sahar" <srohani3.calstatela.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] adding counterions in cpptraj
Message-ID:
<BYAPR06MB4565D1A99434C25DD30274D3E7E29.BYAPR06MB4565.namprd06.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Hi Dan,
Thanks for your response.
Best regards,
Sahar
Get Outlook for iOS<
https://aka.ms/o0ukef>
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Tuesday, July 20, 2021 8:43:40 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] adding counterions in cpptraj
Hi,
No. While there are some commands that are related to modifying
systems, Cpptraj is really just for trajectory processing/data
analysis. I think if I started adding general system preparation
commands I'd be asking for a lot of trouble :-). Not that I haven't
been tempted at times...
-Dan
On Mon, Jul 19, 2021 at 4:48 PM Rohanizeidanlou, Sahar
<srohani3.calstatela.edu> wrote:
>
> Hello Amber Team,
>
> Is there anyway to add counterions in cpptraj to make the net charge zero? I know tleap has good functions to accomplish this, but I was wondering if there's an easier way to do this in cpptraj directly.
>
> Thanks for your support in advance.
>
> Best regards,
> Sahar
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7Csrohani3%40calstatela.edu%7C0744084a9192476ea84508d94b95326e%7Cce8a2002448f4f5882b1d86f73e3afdd%7C0%7C0%7C637623926439033584%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mUn6EkgFzQGmh6Et5FFn4kw6FiFyguaXNyVSQcRjRK0%3D&reserved=0
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------------------------------
Subject: Digest Footer
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End of AMBER Digest, Vol 3428, Issue 1
**************************************
------------------------------
Message: 2
Date: Tue, 20 Jul 2021 19:29:00 -0300
From: "Hector A. Baldoni" <hbaldoni.unsl.edu.ar>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tleap does not recognize inosine
Message-ID: <83668c3c9fed24aa636b39519306235b.unsl.edu.ar>
Content-Type: text/plain; charset=UTF-8; format=flowed
Hello Thamires,
The best practice could be to obtain your ligand from the parameters
developed by F. Lankas et al. for deoxy-inosine in:
1)
http://amber.manchester.ac.uk/
2) Nucleic Acid
3) deoxy-inosine (di)
Best regards,
Hector.
El 2021-07-20 18:42, Thamires Rocco Machado escribi?:
> Thank you very much for your response.
>
> inosine is standalone as a nucleoside, so I will need to make my own
> parameters. Would you have any clue on how could I do it?
>
> I tried with the antechamber too using gaff2, but it also failed to
> generate the force field.
>
> Any help would be appreciated.
>
> Thank you!
>
> Regards,
> Thamires
>
>
--------------------------------------
Dr. Hector A. Baldoni
Profesor Titular (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
------------------------------
Message: 3
Date: Tue, 20 Jul 2021 19:09:35 -0400
From: Ross Walker <ross.rosswalker.co.uk>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cudaMemcpy GpuBuffer ERROR
Message-ID: <433ED9F7-14F0-4649-80D6-C5501E0DBC1F.rosswalker.co.uk>
Content-Type: text/plain; charset=utf-8
Hi Gera,
Power supply is often an issue if it isn't beefy enough but another thing that can cause the behavior you see is a bad PCI-E riser, either on the motherboard or as an adapter that provides for multiple PCI-E slots. As such you may want to try a different PCI-E slot if you can. Although I would also try ruling out the power supply first.
All the best
Ross
> On Jul 20, 2021, at 12:15, Gerardo Zerbetto De Palma <g.zerbetto.gmail.com> wrote:
>
> Plot twist & update:
> We managed to perform the GPU swap and, for now, it appears that the
> problem is the power supply. The TITAN V GPU is now in a computer with
> better (80+ bronze) power supply and has been running during the last 24
> hours without any kind of problem. On the contrary, the RTX2080 GPU that is
> now in the former TITAN V computer, has crashed after running for 12 hours.
> Remarkably, no cudaMemcpy error appeared in the output, but it seemed that
> the hard drive could't be accessed at all. We are going to run some
> additional tests just to confirm this, but it is clear that the problem is
> not in the code nor the GPU nor the simulated system.
> Thank you all for all the help!
> Regards
> Gera!
>
> El lun, 19 jul 2021 a las 12:13, Gerardo Zerbetto De Palma (<
> g.zerbetto.gmail.com>) escribi?:
>
>> We tried older simulations that we had run on GTX1080 and RTX2080 and they
>> all show the same problem. Another remarkable thing is that we had run
>> similar simulations in the TITAN V without any trouble, and this type of
>> crash started to appear more often. Additionally, when the sim crashes,
>> also the whole computer crashes and we have to force reboot it. That is why
>> we will try to swap the GPUs.
>> Thanks a lot, Carlos!?
>> Regards
>>
>> El lun, 19 jul 2021 a las 12:04, Carlos Simmerling (<
>> carlos.simmerling.gmail.com>) escribi?:
>>
>>> that's interesting that it sounds like it is the GPU and not the system
>>> setup itself. Do other simulations of similar size work ok on the Titan V?
>>>
>>> On Mon, Jul 19, 2021 at 11:00 AM Gerardo Zerbetto De Palma <
>>> g.zerbetto.gmail.com> wrote:
>>>
>>>> Hi Carlos. Thanks for the help. The system we are trying to simulate is
>>> a
>>>> nPT membrane embedded protein tetramer. We are just running a plain MD
>>> sim,
>>>> so no additional parameters are set. The initial coordinates were
>>> obtained
>>>> from a previous simulation that we had run with the same parameters, so
>>>> those coordinates are from a very well thermalized system. We just made
>>> a
>>>> single point mutation and made a minimization just to relax any
>>> clashes. It
>>>> is quite remarkable that the same system is being simulated in an
>>> RTX2080
>>>> (in another computer) without any trouble but when we run it in the
>>> TITAN V
>>>> it randomly crashes. Now we will try swapping the GPUs just to discard
>>> that
>>>> it is not a problem with any other computer component.
>>>> Thanks a lot, again.
>>>> Regards
>>>>
>>>> The original post was this one:
>>>> *Hi everyone.*
>>>> *We were trying to run some simulations of a membrane protein on an
>>> NVIDIA
>>>> TITAN V and got stuck by some cudaMemcpy that came in different
>>> flavors:*
>>>>
>>>>
>>>>
>>>> *cudaMemcpy GpuBuffer::Upload failed unspecified launch
>>> failurecudaMemcpy
>>>> GpuBuffer::Download failed unspecified launch failure*
>>>>
>>>> *cudaMemcpy GpuBuffer::Download failed an illegal instruction was
>>>> encountered*
>>>>
>>>> *Firstly we started running the sim using amber 18, restarting the sim
>>>> every 5 nanoseconds to get consecutive 5ns trajectories. After
>>> simulating
>>>> 25 nanoseconds, the program stopped randomly. Then we tried to repeat
>>> the
>>>> simulation that had failed (using the same random seed and initial
>>>> coordinates) and the simulation succeeded, but the same error came up
>>> in a
>>>> subsequent simulation. These errors kept coming at a random timestep
>>> when
>>>> we restarted the simulations. Energies in the output seemed to be OK and
>>>> simulations sometimes proceeded without errors when restarted. Hoping
>>> that
>>>> this was a bug, we compiled amber 20 and ran the same simulations and
>>> had
>>>> the same random cudaMemcpy errors. Just to check if the simulated system
>>>> was fine, we are also running it in a RTX2080 with amber 18 without
>>>> problems, so far.*
>>>>
>>>> *We are running out of ideas here so here we are reaching out to the
>>>> community for some help in this matter. We will appreciate every idea or
>>>> question that can enlighten us to solve this puzzle.*
>>>>
>>>> El lun, 19 jul 2021 a las 11:08, Carlos Simmerling (<
>>>> carlos.simmerling.gmail.com>) escribi?:
>>>>
>>>>> for ff19SB problems, make sure your Amber version is completely
>>> updated
>>>>> with current patches. There was a fix a while back that corrected an
>>>> error
>>>>> that could lead to failures with some force fields including ff19SB.
>>>>> Information on applying patches is found here:
>>>>> http://ambermd.org/AmberPatches.php
>>>>>
>>>>> for the problem with ff14SB, I did not see the original post. More
>>>> details
>>>>> would be helpful, especially about the system you are simulating (is
>>> it
>>>>> only protein, or more? did you use any other parameters except ff14SB?
>>>>> Where were the initial coordinates obtained?).
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jul 19, 2021 at 9:46 AM Gerardo Zerbetto De Palma <
>>>>> g.zerbetto.gmail.com> wrote:
>>>>>
>>>>>> Hi we are using ff14SB forcefield and the errors still appear.
>>>>>> Thanks for the help!
>>>>>> Regards
>>>>>>
>>>>>> Gerardo Zerbetto
>>>>>>
>>>>>> <
>>>>>>
>>>>>
>>>>
>>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>>>>>>>
>>>>>> Virus-free.
>>>>>> www.avg.com<http://www.avg.com>
>>>>>> <
>>>>>>
>>>>>
>>>>
>>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>>>>>>>
>>>>>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>>>>>
>>>>>> El vie, 16 jul 2021 a las 18:29, Rafa? Madaj (<rmadaj.cbmm.lodz.pl
>>>> )
>>>>>> escribi?:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Which force field are you using? I had exactly same problem with
>>>>> ff19SB.
>>>>>>> After changing into ff14SB the problem disappeared.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Rafal
>>>>>>>
>>>>>>> On 16.07.2021 18:01, Gerardo Zerbetto De Palma wrote:
>>>>>>>> Hi everyone.
>>>>>>>> We were trying to run some simulations of a membrane protein on
>>> an
>>>>>> NVIDIA
>>>>>>>> TITAN V and got stuck by some cudaMemcpy that came in different
>>>>>> flavors:
>>>>>>>>
>>>>>>>> cudaMemcpy GpuBuffer::Upload failed unspecified launch failure
>>>>>>>> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>>>>>>>> cudaMemcpy GpuBuffer::Download failed an illegal instruction was
>>>>>>> encountered
>>>>>>>>
>>>>>>>> Firstly we started running the sim using amber 18, restarting
>>> the
>>>> sim
>>>>>>> every
>>>>>>>> 5 nanoseconds to get consecutive 5ns trajectories. After
>>> simulating
>>>>> 25
>>>>>>>> nanoseconds, the program stopped randomly. Then we tried to
>>> repeat
>>>>> the
>>>>>>>> simulation that had failed (using the same random seed and
>>> initial
>>>>>>>> coordinates) and the simulation succeeded, but the same error
>>> came
>>>> up
>>>>>> in
>>>>>>> a
>>>>>>>> subsequent simulation. These errors kept coming at a random
>>>> timestep
>>>>>> when
>>>>>>>> we restarted the simulations. Energies in the output seemed to
>>> be
>>>> OK
>>>>>> and
>>>>>>>> simulations sometimes proceeded without errors when restarted.
>>>> Hoping
>>>>>>> that
>>>>>>>> this was a bug, we compiled amber 20 and ran the same
>>> simulations
>>>> and
>>>>>> had
>>>>>>>> the same random cudaMemcpy errors. Just to check if the
>>> simulated
>>>>>> system
>>>>>>>> was fine, we are also running it in a RTX2080 with amber 18
>>> without
>>>>>>>> problems, so far.
>>>>>>>>
>>>>>>>> We are running out of ideas here so here we are reaching out to
>>> the
>>>>>>>> community for some help in this matter. We will appreciate every
>>>> idea
>>>>>> or
>>>>>>>> question that can enlighten us to solve this puzzle.
>>>>>>>>
>>>>>>>> Regards!
>>>>>>>> Gerardo Zerbetto De Palma
>>>>>>>>
>>>>>>>> <
>>>>>>>
>>>>>>
>>>>>
>>>>
>>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>>>>>>>>
>>>>>>>> Virus-free.
>>>>>>>> www.avg.com<http://www.avg.com>
>>>>>>>> <
>>>>>>>
>>>>>>
>>>>>
>>>>
>>> http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>>>>>>>>
>>>>>>>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 4
Date: Tue, 20 Jul 2021 21:03:19 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tleap does not recognize inosine
Message-ID:
<20210721010319.dokq4anmyuqycjsj.n7230-owl120-03.rad.rutgers.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Tue, Jul 20, 2021, Thamires Rocco Machado wrote:
>
>I tried with the antechamber too using gaff2, but it also failed to
>generate the force field.
Other suggestions on the list are good ones. But if you want to pursue
making your own force field, just saying "failed" doesn't allow anyone to
offer help. You need to say what you tried, and what the result was.
....dac
[As a wild guess: do have all hydrogens on your input structure?]
------------------------------
Message: 5
Date: Tue, 20 Jul 2021 21:06:57 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Gas phase Simulations
Message-ID:
<20210721010657.okorbhna4vb5llyl.n7230-owl120-03.rad.rutgers.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Tue, Jul 20, 2021, Kolattukudy P. Santo wrote:
>Is it useful to use ntp=1, ie pressure coupling, in gas phase simulations
>for polymer ( that is without solvent) in the equilibration stage like in
>http://ambermd.org/tutorials/advanced/tutorial27/pet.htm ?
>Does that make any change over an NVT simulation at the same conditions ?
(a) running constant pressure for a gas-phase simulation indeed makes no
sense: the internal pressure comes mostly from the solvent.
(b) As far as I can see, in the tutorial you cite, the simulations not only
have ntp=0, but they have ntb=0 as well, which is correct: without solvent,
one almost always wants to carry out a non-periodic simulation.
....dac
------------------------------
Message: 6
Date: Tue, 20 Jul 2021 21:21:09 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] 3D-RISM in amber20
Message-ID:
<20210721012109.u42cst6nimxgybyt.n7230-owl120-03.rad.rutgers.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Tue, Jul 20, 2021, Priya Dey wrote:
>The following error is coming: *ERROR: a RESTART or TRAJ file is required*
>
>*In the amber20 manual, it is written the required inputs are "pdb file,
>prmtop file and xvv file". *
>So my query is (a) why is this error coming?
I don't know the answer to this one. I think a pdb file should be allowed,
provided that it was created by something like ambpdb, so that the order of
atoms is the same as in the prmtop file. But ambpdb requires a restart
or trajectory file, so requiring one of the latter is not supposed to be a big
burdern.
>(b) If a restart file has to be used, which restart file should I use? (as
>I have tried with the initial restart file that is generated during system
>preparation: in that case the system is reading coordinates from the
>restart file whatever the pdb is given, and the output is similar for
>different pdbs.)
If you have done anything after the initial system prepartaion
(minimization, dynamics), you should have a restart file that corresponds to
the end of such a run. You need to choose a file that has the coordinates
you wish to use.
If you just have a generic PDB file (not coming from Amber) you will
probably need to feed that to tleap in order to obtain the desired restart
file.
...hope this helps....dac
------------------------------
Message: 7
Date: Wed, 21 Jul 2021 01:23:34 +0000
From: Razil Tahir <raziltahir.hotmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Message-ID:
<SI2PR06MB447496DF73DFF2D75A0168C1C5E39.SI2PR06MB4474.apcprd06.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi, Dr.
Here is the email from the mailing list.
Thank you,
Razil.
________________________________
From: Dr. Anselm Horn <anselm.horn.fau.de>
Sent: Monday, July 19, 2021 5:11 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Razil,
some time ago we used a (somehow) similar system, namely trehalose with
two acyl chains. To be consistent within the ligand system (and to avoid
any cross-terms between forcefield borders), we decided to use only
Glycam atom types there and applied the Glycam charge parameterization
scheme.
If you are interested, have a look into the Supplementary material there:
https://doi.org/10.1038/s41598-018-23624-8
But I guess, St?phane's work might be more related to your ligand system.
Good luck,
Anselm
On 07/18/2021 07:02 PM, Razil Tahir wrote:
> Hello experts,
> I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
> I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
> Is this method practical and correct to be used? Please advise.
>
> Thank you.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 8
Date: Wed, 21 Jul 2021 01:33:01 +0000
From: tluchko <tluchko.protonmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] 3D-RISM in amber20
Message-ID:
<kfe4LnGNLYO0jGw3b-ZZhkTRfbJpVg7UnSpfeOkno6BcgYLlM3UUxcM2zp52f2CgeYEHaeUTyekwFYX.com>
Content-Type: text/plain; charset=utf-8
Hi Priya,
The behavior change sometime before Amber 19. I'm not sure why and the change didn't make it into the manual.
Though it adds an extra step, the workaround is quite straightforward. You can create a restart file or single frame .nc trajectory file using cpptraj. E.g.,
cpptraj -p parameterfile -y pdbname -x restart_or_traj_name
The resulting file will have identical coordinates to your PDB file (which you still need to include).
Hope this helps,
Tyler
Sent with ProtonMail Secure Email.
??????? Original Message ???????
On Monday, July 19th, 2021 at 11:35 PM, Priya Dey <mmv.priya.dey.gmail.com> wrote:
> Initially, we were using amber 12 for 3D-RISM calculation using
>
> rism3d.snglpnt.MPI
>
> command.
>
> Then, we have updated the amber12 software to amber20. We have tried to run
>
> the following script for 3d rism calculation-
>
> rism3d.snglpnt.MPI --pdb pdbname --prmtop parameterfie --closure kh
>
> --buffer -1 --solvcut 32 --verbose 2 --xvv SPC-1D.xvv --solvbox
>
> 128,128,128 --ng 256,256,256 --grdspc 0.5,0.5,0.5 > logfile
>
> the SPC-1d.xvv file is generated using 1D RISM.
>
> The following error is coming: ERROR: a RESTART or TRAJ file is required
>
> *In the amber20 manual, it is written the required inputs are "pdb file,
>
> prmtop file and xvv file". *
>
> So my query is (a) why is this error coming?
>
> (b) If a restart file has to be used, which restart file should I use? (as
>
> I have tried with the initial restart file that is generated during system
>
> preparation: in that case the system is reading coordinates from the
>
> restart file whatever the pdb is given, and the output is similar for
>
> different pdbs.)
>
> (c) If a traj file has to be used, which traj file should I use?
>
> Priya Dey
>
> Research Scholar
>
> c/o Prof. Parbati Biswas
>
> *Department of Chemistry *
>
> University of Delhi
>
> Delhi,110007
>
> India
>
> Contact Number-8010903736
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 9
Date: Wed, 21 Jul 2021 01:36:13 +0000
From: Razil Tahir <raziltahir.hotmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Message-ID:
<SI2PR06MB4474E6E83B365FC33081F098C5E39.SI2PR06MB4474.apcprd06.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi, Dr.
Thank you for the response.
I've tried to use CT atomtype from the GLYCAM for the acyl chain but when I ran parmchk and generated the frcmod file, there are angles, bonds and dihedral angles that requires attention (ATTN, need revision).
How do you resolve this and where should I refer to get the values?
Thank you, Dr.
Razil.
________________________________
From: Dr. Anselm Horn <anselm.horn.fau.de>
Sent: Monday, July 19, 2021 5:11 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Razil,
some time ago we used a (somehow) similar system, namely trehalose with
two acyl chains. To be consistent within the ligand system (and to avoid
any cross-terms between forcefield borders), we decided to use only
Glycam atom types there and applied the Glycam charge parameterization
scheme.
If you are interested, have a look into the Supplementary material there:
https://doi.org/10.1038/s41598-018-23624-8
But I guess, St?phane's work might be more related to your ligand system.
Good luck,
Anselm
On 07/18/2021 07:02 PM, Razil Tahir wrote:
> Hello experts,
> I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
> I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
> Is this method practical and correct to be used? Please advise.
>
> Thank you.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 10
Date: Wed, 21 Jul 2021 01:38:42 +0000
From: Razil Tahir <raziltahir.hotmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Message-ID:
<SI2PR06MB447482FE6D767FF0A044554FC5E39.SI2PR06MB4474.apcprd06.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Hi, Dr.
Thank you for the response.
I've tried to use CT atomtype from the GLYCAM for the acyl chain but when I ran parmchk and generated the frcmod file, there are angles, bonds and dihedral angles that requires attention (ATTN, need revision).
How do you resolve this and where should I refer to get the values?
My next question is why did you choose RESP for the charges?
Thank you, Dr.
Razil.
________________________________
From: ABEL Stephane <Stephane.ABEL.cea.fr>
Sent: Monday, July 19, 2021 4:56 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Hello
You could take a look of my paper see
1. Abel S, Dupradeau F-YY, Raman EP, MacKerell AD, Marchi M. 2011 Molecular simulations of dodecyl-?-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J. Phys. Chem. B 115, 487?499. (doi:10.1021/jp109545v)
I developed RESP charges for glycolipids and used them with GLYCAM parameters
Good luck
St?phane
________________________________________
De : Razil Tahir [raziltahir.hotmail.com]
Envoy? : dimanche 18 juillet 2021 19:02
? : AMBER Mailing List
Objet : [AMBER] Building Forcefield for Glycolipid Molecule
Hello experts,
I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
Is this method practical and correct to be used? Please advise.
Thank you.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 11
Date: Tue, 20 Jul 2021 21:55:57 -0400
From: "Kolattukudy P. Santo" <santotheophys.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Gas phase Simulations
Message-ID:
<CAAoy1or0Q6EKZhS-Yr-EkgePwD_5xk2YN6QO1ySYLD9Op_esww.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Thanks David,
I have periodic bcs and ntp=1, then the system should relax to solid phase.
Santo
On Tue, 20 Jul 2021 at 21:07, David A Case <dacase.chem.rutgers.edu> wrote:
> On Tue, Jul 20, 2021, Kolattukudy P. Santo wrote:
>
> >Is it useful to use ntp=1, ie pressure coupling, in gas phase simulations
> >for polymer ( that is without solvent) in the equilibration stage like
> in
> >http://ambermd.org/tutorials/advanced/tutorial27/pet.htm ?
> >Does that make any change over an NVT simulation at the same conditions ?
>
> (a) running constant pressure for a gas-phase simulation indeed makes no
> sense: the internal pressure comes mostly from the solvent.
>
> (b) As far as I can see, in the tutorial you cite, the simulations not only
> have ntp=0, but they have ntb=0 as well, which is correct: without
> solvent,
> one almost always wants to carry out a non-periodic simulation.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
---------------------------------------------------------
------------------------------
Message: 12
Date: Tue, 20 Jul 2021 21:29:30 -0500
From: Pengfei Li <ambermailpengfei.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Missing mtkpp directory after installation of
AmberTools21
Message-ID: <E86DE5DC-8F9C-4FBB-B6DB-80BE98378291.gmail.com>
Content-Type: text/plain; charset=us-ascii
Hi Anthony,
As Dave said, the new version of AmberTools does not have MCPB in it.
MCPB.py has a different usage from MCPB, which means it does not need the genMetalFF.sh script anymore.
Here are two tutorials for MCPB.py: https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php>, https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php>.
Hope it helps,
Pengfei
> On Jul 20, 2021, at 9:55 AM, Anthony Nash <anthony.nash.ndcn.ox.ac.uk> wrote:
>
> In answer to my own question, I created a new environment and I've downloaded and installed AmberTools21 from source.
>
> However, having now looked through the manual pdf, and compared it to the HTML page dating 2015 which begins with running genMetalFF.sh, all of the required variables for MCPB.py aren't in the bcl files that genMetalFF originally generated.
>
> Rather than hack around hoping something will work, is there a latest and greater bonded model tutorial specifically designed with the latest MCPB.py in mind?
>
> Thanks
> Anthony
>
> Kind regards
> Dr Anthony Nash PhD MRSC
>
> Senior Research Scientist
> Nuffield Department of Clinical Neurosciences
> RMCR Kellogg College
> University of Oxford
> http://www.kellogg.ox.ac.uk/
>
> ________________________________
> From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
> Sent: 19 July 2021 14:37
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Missing mtkpp directory after installation of AmberTools21
>
> Dear all,
>
> I'm a new user of AMBER but a long time MD modeller and I'm hoping I can get some help resolving a post-installation concern over what and where some of the files are.
>
> I am trying to step through the bonded metal-binding centre tutorials given here: https://ambermd.org/tutorials/advanced/tutorial20/mcpb.php
>
> The only difference is that I'm using my own set of pdb files. Six in total; two zinc-based and four calcium-based coordination centres.
>
> I installed AmberTools21 in Linux (in fact, it was WSL2 Ubuntu) using conda. The installation didn't flag up any problems.
>
> These are my concerns/issues:
>
> Firstly, as per the tutorial linked above, I wasn't able to find genMetalFF.sh in my AMBERHOME directory structure. So, I downloaded the file from the link provided in the tutorial and generated the corresponding setup files for MCPB.
>
> Then, the next slight concern I ran into was upon investigating zinc_1201_settings.bcl (one of my generated files) I noticed the directory structure AMBERHOME/dat/mtkpp/ is missing!
>
> Finally, before resorting to this email, I was unable to find the MCPB executable. Instead, I'm able to find MCPB.py (of which, I've noticed the command line arguments are slightly different to the command line arguments of MCP B). Either way, I decided to execute the python executable and I got the following error:
>
> Traceback (most recent call last):
> File "/home/ubuntu/miniconda3/envs/AmberTools21/bin/MCPB.py", line 67, in <module>
> options.step = options.step.lower()
> AttributeError: 'NoneType' object has no attribute 'lower'
>
>
> All suggestions are welcome.
>
> Many thanks
> Anthony
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 13
Date: Wed, 21 Jul 2021 13:27:51 +0530
From: Jenny 148 <jenny.rs140.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] pc1 vs pc2 principal component analysis
Message-ID:
<CAPFYAV9pyCt2shPsQDc0E4Ve+M8jrtcJfpg8067Z7r2TSdAPcQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
>> It's not clear what you mean here - which file had 11 columns? Can you
post the exact input you are using, and point out the file that you
unsure about that has 11 columns?
This is the command line I have used
diagmatrix systemcovar out evectors.dat vecs 20 nmwiz nmwizvecs 5
nmwizfile system.nmd nmwizmask :
1-831.CA
>>>Yes. You are projecting the coordinates of CA atoms of residues 1-831
on the eigenvectors read in from evectors.dat (presumably generated
from the same coordinate selection), only for eigenvectors (modes) 1
and 2
So In that case, in my PC1 vs PC2, each point represents one frame?
On Tue, 20 Jul 2021 at 23:41, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Jul 16, 2021 at 3:43 PM Jenny 148 <jenny.rs140.gmail.com> wrote:
> > I am working with a protein system. I have constructed the
> > diagonalized coordinate covariance matrix for eigenmodes in a file
> > evectors.dat with the command line being beg 1 end 20 (though I had only
> 11
> > columns, the reason of which I am not sure. After that using the
> following
>
> It's not clear what you mean here - which file had 11 columns? Can you
> post the exact input you are using, and point out the file that you
> unsure about that has 11 columns?
>
> > readdata evectors.dat name Modes
> > # Now create separate PC projections for each trajectory
> > projection A1 modes Modes out pca12-ca beg 1 end 2 :1-831.CA
> >
> > After which I get a file pca12-ca, which looked somewhat like this:
> > #Frame Mode1 Mode2
> > 1 36.824 5.205
> > 2 35.917 5.359
> > 3 34.797 6.404
> > 4 34.637 8.611
> > 5 35.224 9.040
> > ...........(Blanking out the rest)
> >
> > My query is whether the pca12-ca file which I got, the actual PC1 vs PC2
> > file? I mean, would plotting the 2nd and 3rd column in the above file
> as X
> > and Y axis, allow me to get a scatter plot between the First and second
>
> Yes. You are projecting the coordinates of CA atoms of residues 1-831
> on the eigenvectors read in from evectors.dat (presumably generated
> from the same coordinate selection), only for eigenvectors (modes) 1
> and 2.
>
> Hope this helps,
>
> -Dan
>
> > principal component of my trajectory?
> >
> > --
> > Jenny R.S
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jenny R.S
Sir Syed College,
Taliparamba,
Kannur,
Kerala
------------------------------
Message: 14
Date: Wed, 21 Jul 2021 10:55:30 +0200
From: "Dr. Anselm Horn" <anselm.horn.fau.de>
To: <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Message-ID: <62e52188-ddae-260a-1259-b35dd778d3a8.fau.de>
Content-Type: text/plain; charset="utf-8"
Razil,
the choice of atom types in a unit to be parameterized is crucial for
its forcefield description, since from the combination of bonded atoms,
triples (angle terms), and quadruples (torsion terms) it is determined,
whether force field parameters already exist or not.
We did not use atom type CT for our approach for acyl chain atoms;
like Stephan?, we used a RESP charge generation approach (via the
RED-Server), similar to the orginal Glycam philosophy. This is all
described in detail in the Supplementary Material of our manuscript.
If parameters are missing or marked as need revision, parameters from
similar terms may potentially be used. Then, however, test simulations
should be run to ensure the validity of this approach.
Good luck
Anselm
On 07/21/2021 03:36 AM, Razil Tahir wrote:
> Hi, Dr.
> Thank you for the response.
>
> I've tried to use CT atomtype from the GLYCAM for the acyl chain but when I ran parmchk and generated the frcmod file, there are angles, bonds and dihedral angles that requires attention (ATTN, need revision).
>
> How do you resolve this and where should I refer to get the values?
>
> Thank you, Dr.
>
> Razil.
>
> ________________________________
> From: Dr. Anselm Horn <anselm.horn.fau.de>
> Sent: Monday, July 19, 2021 5:11 PM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
>
> Razil,
>
> some time ago we used a (somehow) similar system, namely trehalose with
> two acyl chains. To be consistent within the ligand system (and to avoid
> any cross-terms between forcefield borders), we decided to use only
> Glycam atom types there and applied the Glycam charge parameterization
> scheme.
>
> If you are interested, have a look into the Supplementary material there:
> https://doi.org/10.1038/s41598-018-23624-8
>
> But I guess, St?phane's work might be more related to your ligand system.
>
> Good luck,
>
> Anselm
>
>
> On 07/18/2021 07:02 PM, Razil Tahir wrote:
>> Hello experts,
>> I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
>> I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
>> Is this method practical and correct to be used? Please advise.
>>
>> Thank you.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 15
Date: Wed, 21 Jul 2021 09:35:16 +0000
From: ABEL Stephane <Stephane.ABEL.cea.fr>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Message-ID: <cb7d1deeb9104bf59b0f8cb0a2196ca9.cea.fr>
Content-Type: text/plain; charset="utf-8"
Hello,
If you cannot use the CT atom type for your model (without further optimisation) you could use the glycam web server to get the parameters by analogy
http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1
For the RESP charges, as anselm.horn, we used the RED server and followed the GLYCAM philosophy (your could read the SI of our paper too)
HTH
St?phane
----------------------------------------------------------
St?phane Abel, Ph.D., HDR
CEA Centre de Saclay
DRF/JOLIOT/I2BC-S/SB2SM/LBMS
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Razil Tahir [raziltahir.hotmail.com]
Envoy? : mercredi 21 juillet 2021 03:38
? : AMBER Mailing List
Objet : Re: [AMBER] Building Forcefield for Glycolipid Molecule
Hi, Dr.
Thank you for the response.
I've tried to use CT atomtype from the GLYCAM for the acyl chain but when I ran parmchk and generated the frcmod file, there are angles, bonds and dihedral angles that requires attention (ATTN, need revision).
How do you resolve this and where should I refer to get the values?
My next question is why did you choose RESP for the charges?
Thank you, Dr.
Razil.
________________________________
From: ABEL Stephane <Stephane.ABEL.cea.fr>
Sent: Monday, July 19, 2021 4:56 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Hello
You could take a look of my paper see
1. Abel S, Dupradeau F-YY, Raman EP, MacKerell AD, Marchi M. 2011 Molecular simulations of dodecyl-?-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J. Phys. Chem. B 115, 487?499. (doi:10.1021/jp109545v)
I developed RESP charges for glycolipids and used them with GLYCAM parameters
Good luck
St?phane
________________________________________
De : Razil Tahir [raziltahir.hotmail.com]
Envoy? : dimanche 18 juillet 2021 19:02
? : AMBER Mailing List
Objet : [AMBER] Building Forcefield for Glycolipid Molecule
Hello experts,
I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
Is this method practical and correct to be used? Please advise.
Thank you.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 16
Date: Wed, 21 Jul 2021 13:10:41 +0000
From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Missing mtkpp directory after installation of
AmberTools21
Message-ID:
<LO2P265MB260707D19870B8ECEC8ED78B89E39.LO2P265MB2607.GBRP265.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="us-ascii"
Hi Pengfei,
Thank you for clearing this up.
Perhaps opening up the actual scientific dilemma behind my enquiry might prove fruitful.
I'm attempting to parameterise 4 calcium ions and 2 zinc ions in a metalloprotease. The last time I parameterised metal for a protein was quite a few years ago and I did it by writing my own 2nd derivative of the Hessian-based model using a Gaussian log file. Unfortunately, I don't have access to a Gaussian license anymore. I've requested a GAMESS-US license, but I've never used that before.
Are there any empirical calculations I can perform to derive force constants? To satisfy charges I believe I can still use the RED server.
Thanks
Anthony
Kind regards
Dr Anthony Nash PhD MRSC
Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/
________________________________
From: Pengfei Li <ambermailpengfei.gmail.com>
Sent: 21 July 2021 03:29
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Missing mtkpp directory after installation of AmberTools21
Hi Anthony,
As Dave said, the new version of AmberTools does not have MCPB in it.
MCPB.py has a different usage from MCPB, which means it does not need the genMetalFF.sh script anymore.
Here are two tutorials for MCPB.py: https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php>, https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php <https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php>.
Hope it helps,
Pengfei
> On Jul 20, 2021, at 9:55 AM, Anthony Nash <anthony.nash.ndcn.ox.ac.uk> wrote:
>
> In answer to my own question, I created a new environment and I've downloaded and installed AmberTools21 from source.
>
> However, having now looked through the manual pdf, and compared it to the HTML page dating 2015 which begins with running genMetalFF.sh, all of the required variables for MCPB.py aren't in the bcl files that genMetalFF originally generated.
>
> Rather than hack around hoping something will work, is there a latest and greater bonded model tutorial specifically designed with the latest MCPB.py in mind?
>
> Thanks
> Anthony
>
> Kind regards
> Dr Anthony Nash PhD MRSC
>
> Senior Research Scientist
> Nuffield Department of Clinical Neurosciences
> RMCR Kellogg College
> University of Oxford
> http://www.kellogg.ox.ac.uk/
>
> ________________________________
> From: Anthony Nash <anthony.nash.ndcn.ox.ac.uk>
> Sent: 19 July 2021 14:37
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: Missing mtkpp directory after installation of AmberTools21
>
> Dear all,
>
> I'm a new user of AMBER but a long time MD modeller and I'm hoping I can get some help resolving a post-installation concern over what and where some of the files are.
>
> I am trying to step through the bonded metal-binding centre tutorials given here: https://ambermd.org/tutorials/advanced/tutorial20/mcpb.php
>
> The only difference is that I'm using my own set of pdb files. Six in total; two zinc-based and four calcium-based coordination centres.
>
> I installed AmberTools21 in Linux (in fact, it was WSL2 Ubuntu) using conda. The installation didn't flag up any problems.
>
> These are my concerns/issues:
>
> Firstly, as per the tutorial linked above, I wasn't able to find genMetalFF.sh in my AMBERHOME directory structure. So, I downloaded the file from the link provided in the tutorial and generated the corresponding setup files for MCPB.
>
> Then, the next slight concern I ran into was upon investigating zinc_1201_settings.bcl (one of my generated files) I noticed the directory structure AMBERHOME/dat/mtkpp/ is missing!
>
> Finally, before resorting to this email, I was unable to find the MCPB executable. Instead, I'm able to find MCPB.py (of which, I've noticed the command line arguments are slightly different to the command line arguments of MCP B). Either way, I decided to execute the python executable and I got the following error:
>
> Traceback (most recent call last):
> File "/home/ubuntu/miniconda3/envs/AmberTools21/bin/MCPB.py", line 67, in <module>
> options.step = options.step.lower()
> AttributeError: 'NoneType' object has no attribute 'lower'
>
>
> All suggestions are welcome.
>
> Many thanks
> Anthony
>
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Message: 17
Date: Wed, 21 Jul 2021 09:57:07 -0400
From: David A Case <dacase.chem.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Gas phase Simulations
Message-ID:
<20210721135707.hqkx6v6huwps7wxq.n7230-owl120-03.rad.rutgers.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Tue, Jul 20, 2021, Kolattukudy P. Santo wrote:
>I have periodic bcs and ntp=1, then the system should relax to solid phase.
Your email subject said "gas phase simulation", so I was replying to that.
You can indeed do crystal simulations, but "relax[ing] to the solid phase"
is something I've not seen. For sure, start a first simulation with atomic
coordinates near what you expect the final result to be, to get experience
about what to expect.
I expect it will be extremely tricky to get an ntp=1 simulation to go from a
gas-phase volume to a solid-phase volume. (Put in other words, I don't
think current codes can do it, but I've never tried myself.)
...dac
------------------------------
Message: 18
Date: Wed, 21 Jul 2021 20:57:08 +0530
From: "Amit Sharma (Asstt. Prof., MCARS)" <asharma4.jmi.ac.in>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Displacement of coordinated Zn during the simulation
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<CAC9mRRkHVW37XuhqR9S7M_Qqow4FjnRye=Qj0vkAkR1++cM=Qg.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
Cysteine coordinated Zn ion have got displaced from it's positions during
the MD run when the protein was subjected to certain external perturbation.
I wonder, if through the MD simulation can we also expect to see that the
displaced Zn ion will move back to it's normal coordination position, once
we remove the external perturbation?
Any suggestions (or references of MD simulation work using Amber) may be
helpful in which the movement of the coordinated ions (influenced by the
application or removal of any external perturbation on the protein system)
in or out of their coordination geometry has been observed previously.
Thank You,
Amit
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Message: 19
Date: Wed, 21 Jul 2021 13:38:19 -0400
From: "Kolattukudy P. Santo" <santotheophys.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Gas phase Simulations
Message-ID:
<CAAoy1oqw2Lc7PU-fjWge365yXAQW1+z_J59x_R5qX3yQ9iAsiw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Thanks David again, for the useful comments.
Santo
On Wed, 21 Jul 2021 at 09:57, David A Case <dacase.chem.rutgers.edu> wrote:
> On Tue, Jul 20, 2021, Kolattukudy P. Santo wrote:
>
> >I have periodic bcs and ntp=1, then the system should relax to solid
> phase.
>
> Your email subject said "gas phase simulation", so I was replying to that.
>
> You can indeed do crystal simulations, but "relax[ing] to the solid phase"
> is something I've not seen. For sure, start a first simulation with atomic
> coordinates near what you expect the final result to be, to get experience
> about what to expect.
>
> I expect it will be extremely tricky to get an ntp=1 simulation to go from
> a
> gas-phase volume to a solid-phase volume. (Put in other words, I don't
> think current codes can do it, but I've never tried myself.)
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
KP Santo
--------------------------------------------------------------
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
USA
---------------------------------------------------------
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