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--
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
>
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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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
> _______________________________________________
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------------------------------
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
>
>
>
>
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> 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
>> > > > > > 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: 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
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Received on Tue Jul 20 2021 - 15:00:02 PDT