Re: [AMBER] amber 20 compilation problem (David A Case)

From: Jordi Bujons <jordi.bujons.iqac.csic.es>
Date: Fri, 4 Dec 2020 18:30:28 +0100

On Tue, Dec 01, 2020, Jordi Bujons wrote:
>>
>>I am trying to compile amber 20 on a workstation that includes a GTX
>>3090 GPU. The workstation runs CentOS 8 with cuda 11.1 and Nvidia
>>driver version 455.32.00,
>>
>>-- CUDA version 11.1 detected
>> Error: Unsupported CUDA version. AMBER requires CUDA version >= 7.5
>>and <= 11.0.
>
>It's been hard to get Amber cuda developers to spend time on this, but as
far as I know, the following will work:
>
>Go to the cmake directory, and edit the CudaConfig.cmake file. Find the
>line:
>
> elseif(${CUDA_VERSION} VERSION_EQUAL 11.0)
>
>and change it to
>
> elseif(${CUDA_VERSION} VERSION_GREATER_EQUAL 11.0)
>
>...good luck...dac

Yes, your suggestion works! Thanks a lot.

Best,

jordi


------------------------------

Message: 4
Date: Tue, 1 Dec 2020 21:07:17 -0500
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <20201202020717.47fioimezjq2lwhc.Davids-MBP.fios-router.home>
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On Tue, Dec 01, 2020, Gordon Richard Chalmers wrote:
>
>I have a quick question as to how AmberTools20, tleap, or cpptraj
>rotates the molecule about a phi or psi dihedral angle.

The world's experts on this subject are right in your backyard: check with
Rob Woods or Lachele Foley, who probably have the longest institutional
memory about this.

The basic problem is that just saying you want to rotate about an angle is
not enough information. One also needs to specify which atoms (i.e.
which "side" of the torsion) should be moved. But the tleap syntax doesn't
include this, and it can be rather difficult to understand its internal
procedures for making this decision.

I'm less familiar with cpptraj handles this problem.

....dac




------------------------------

Message: 5
Date: Wed, 2 Dec 2020 04:36:39 +0000
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        
<BN6PR02MB27064845AB198F310F36F6AADCF30.BN6PR02MB2706.namprd02.prod.outlook.
com>
        
Content-Type: text/plain; charset="iso-8859-1"

I am going to write this again because the note wasn't read. The atoms are
specified for the rotations.

TLeAP or Cpptraj should be documented in this if we are supposed to do
molecular work using Amber. This topic is a little basic in protein work
and should be documented in Amber.

Also, each 4 atom pair defining 2 planes specify different angular rotations
and should commute. This means the order of the phi/psi rotations in the
residues is independent and commute.

Gordon Chalmers

________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, December 1, 2020 9:07 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


On Tue, Dec 01, 2020, Gordon Richard Chalmers wrote:
>
>I have a quick question as to how AmberTools20, tleap, or cpptraj
>rotates the molecule about a phi or psi dihedral angle.

The world's experts on this subject are right in your backyard: check with
Rob Woods or Lachele Foley, who probably have the longest institutional
memory about this.

The basic problem is that just saying you want to rotate about an angle is
not enough information. One also needs to specify which atoms (i.e.
which "side" of the torsion) should be moved. But the tleap syntax doesn't
include this, and it can be rather difficult to understand its internal
procedures for making this decision.

I'm less familiar with cpptraj handles this problem.

....dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


------------------------------

Message: 6
Date: Wed, 2 Dec 2020 12:47:22 +0530
From: Satyaseelan C <bo17resch11006.iith.ac.in>
Subject: [AMBER] Imaging issue in DNA - cpptraj
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAK7XutpA10jG5cjzg0FyZPqEc1bj=e5BsdtYQdvtZ_qMh4OVMw.mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Amber users,
               I am facing an imaging issue during the MD simulation of a
DNA duplex. Due to this, the RMSD is shooting up and falls back during the
middle of the simulation. I am observing this problem for 50ns during the
simulation. I used autoimage option followed by image option as below:

parm prmtop
trajin trajin.nc
autoimage
center :1-16 origin
image origin center familiar
center :1-32 origin
image origin center familiar
trajout reimage.nc
go

When I don't apply any imaging, the DNA strands are separated and going out
of the box in some frames. But, after performing imaging, the problem is not
completely resolved. Here, a stretch of DNA strand is going away and causes
distortions in the structure for 50ns. I have attached the corresponding
snapshots.

Please suggest any alternative options to overcome this issue.


Thanks in advance
Sathyaseelan

--
*Thanks & Regards*
*C .Sathyaseelan *
*PhD Research Scholar*
*C/o Dr. Thenmalarchelvi Rathinavelan*
*Molecular Biophysics Lab*
*Dept. of Biotechnology*
*Indian Institute of Technology (IIT)*
*Kandi, Hyderabad, Telangana - 502285*
*Ph.No 6383836804, 8300150807*
-- 
Disclaimer:- The information contained in this electronic message and any
attachments to this message are intended for the exclusive use of the
addressee(s) and may contain proprietary, confidential or privileged
information. If you are not the intended recipient, you should not
disseminate, distribute or copy this email. Please notify the sender
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------------------------------
Message: 7
Date: Wed, 2 Dec 2020 08:53:32 +0100
From: Karl Kirschner <k.n.kirschner.gmail.com>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAF=D-bz-j1Y7Qp-7_frB-jzU9DBn61cxdxyYM5-jkdQmwemefA.mail.gmail.com>
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Hi, Richard,
  You can rotate a dihedral in tleap by using the "impose" command. Let's
say you have an tleap object named "mymolecule" that is composed of several
residues, and you want to rotate residue 7's atoms that are named C1, C2,
C3 and C4 to 120 degrees, then the following command should work:
impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
Note that it becomes a bit unclear if you have rotating a dihedral is
between two residues. Then you indicate the lower residue number, and start
the sequence with it's atom names. In the Amber20's manual, you can find
additional examples on page 242 (subsection entitled "Procedures for
building oligosaccharides using the GLYCAM-06 parameters").
An alternative approach is to use PyMol, which would enable you to visually
see the rotation being made and if any atomic clashes happen. To do this you
need to label the atoms via their "ID" and then use the command
"set_dihedral" (e.g. "set_dihedral ID 6, ID 7, ID 8, ID 9, 120") Using PyMol
will add a few steps to your workflow since the resulting structure must be
saved to a PDB-formatted file and then be loaded back into tleap.
However, this approach will help maintain a precise understanding of what is
structurally happening to your molecule with your manual manipulation.
Furthermore, you can create a PyMol script that allows you to encode these
changes and then have a reminder of exactly what you did for your model
building, increasing the reproducibility of the workflow if needed later.
Bests,
Karl
On Wed, Dec 2, 2020 at 3:07 AM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Dec 01, 2020, Gordon Richard Chalmers wrote:
> >
> >I have a quick question as to how AmberTools20, tleap, or cpptraj 
> >rotates the molecule about a phi or psi dihedral angle.
>
> The world's experts on this subject are right in your backyard: check 
> with Rob Woods or Lachele Foley, who probably have the longest 
> institutional memory about this.
>
> The basic problem is that just saying you want to rotate about an 
> angle is not enough information.  One also needs to specify which atoms
(i.e.
> which "side" of the torsion) should be moved.  But the tleap syntax 
> doesn't include this, and it can be rather difficult to understand its 
> internal procedures for making this decision.
>
> I'm less familiar with cpptraj handles this problem.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 8
Date: Wed, 2 Dec 2020 08:12:38 +0000
From: Gustaf Olsson <gustaf.olsson.lnu.se>
Subject: Re: [AMBER] Imaging issue in DNA - cpptraj
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <792960D5-71D0-4DAB-A764-F5561BC21A79.lnu.se>
Content-Type: text/plain; charset="us-ascii"
Short of increasing the solvent buffer to avoid jumps, trying to play around
with the masks for image/autoimage seems reasonable.
See what happens if you autoimage with a mask defined. Either trying to
center the entire DNA or as suggested
(https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small
region of the DNA which should be close to the center of the box.
Best regards
// Gustaf
On 2 Dec 2020, at 08:17, Satyaseelan C
<bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote:
Dear Amber users,
              I am facing an imaging issue during the MD simulation of a DNA
duplex. Due to this, the RMSD is shooting up and falls back during the
middle of the simulation. I am observing this problem for 50ns during the
simulation. I used autoimage option followed by image option as below:
parm prmtop
trajin trajin.nc
autoimage
center :1-16 origin
image origin center familiar
center :1-32 origin
image origin center familiar
trajout reimage.nc
go
When I don't apply any imaging, the DNA strands are separated and going out
of the box in some frames. But, after performing imaging, the problem is not
completely resolved. Here, a stretch of DNA strand is going away and causes
distortions in the structure for 50ns. I have attached the corresponding
snapshots.
Please suggest any alternative options to overcome this issue.
Thanks in advance
Sathyaseelan
--
*Thanks & Regards*
*C .Sathyaseelan *
*PhD Research Scholar*
*C/o Dr. Thenmalarchelvi Rathinavelan*
*Molecular Biophysics Lab*
*Dept. of Biotechnology*
*Indian Institute of Technology (IIT)*
*Kandi, Hyderabad, Telangana - 502285*
*Ph.No 6383836804, 8300150807*
--
Disclaimer:- The information contained in this electronic message and any
attachments to this message are intended for the exclusive use of the
addressee(s) and may contain proprietary, confidential or privileged
information. If you are not the intended recipient, you should not
disseminate, distribute or copy this email. Please notify the sender
immediately and destroy all copies of this message and any attachments. The
views expressed in this E-mail message (including the enclosure/(s) or
attachment/(s) if any) are those of the individual sender, except where the
sender expressly, and with authority, states them to be the views of IIT
Hyderabad. Before opening any mail and attachments please check them for
viruses, malware, and the sender email address is indeed from IITH domain.
IITH does not accept any liability for malware infected mails.
<nowaterbox.png><waterbox.png>______________________________________________
_
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------------------------------
Message: 9
Date: Wed, 2 Dec 2020 10:23:56 +0100
From: "Dr. Anselm Horn" <anselm.horn.fau.de>
Subject: Re: [AMBER] Imaging issue in DNA - cpptraj
To: <amber.ambermd.org>
Message-ID: <33b14e89-7927-8bc7-bfd9-2f97be4c49c9.fau.de>
Content-Type: text/plain; charset="utf-8"
Hi,
just to add a comment:
If you used iwrap=1 in your simulation input, try to use the unwrap command
in cpptraj, expecially, if you are not interested in the solvent
molecules: strip off these first, the do the unwrap and omit the (auto)image
commands.
However, you may want to use a rms fit command to obtain a trajectory better
to visualize.
Regards,
Anselm
On 12/02/2020 09:12 AM, Gustaf Olsson wrote:
> Short of increasing the solvent buffer to avoid jumps, trying to play
around with the masks for image/autoimage seems reasonable.
> 
> See what happens if you autoimage with a mask defined. Either trying to
center the entire DNA or as suggested
(https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small
region of the DNA which should be close to the center of the box.
> 
> Best regards
> // Gustaf
> 
> 
> On 2 Dec 2020, at 08:17, Satyaseelan C
<bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote:
> 
> Dear Amber users,
>               I am facing an imaging issue during the MD simulation of 
> a DNA duplex. Due to this, the RMSD is shooting up and falls back 
> during the middle of the simulation. I am observing this problem for 
> 50ns during the simulation. I used autoimage option followed by image
option as below:
> 
> parm prmtop
> trajin trajin.nc
> autoimage
> center :1-16 origin
> image origin center familiar
> center :1-32 origin
> image origin center familiar
> trajout reimage.nc
> go
> 
> When I don't apply any imaging, the DNA strands are separated and 
> going out of the box in some frames. But, after performing imaging, 
> the problem is not completely resolved. Here, a stretch of DNA strand 
> is going away and causes distortions in the structure for 50ns. I have 
> attached the corresponding snapshots.
> 
> Please suggest any alternative options to overcome this issue.
> 
> 
> Thanks in advance
> Sathyaseelan
> 
> --
> *Thanks & Regards*
> 
> *C .Sathyaseelan *
> *PhD Research Scholar*
> *C/o Dr. Thenmalarchelvi Rathinavelan* *Molecular Biophysics Lab* 
> *Dept. of Biotechnology* *Indian Institute of Technology (IIT)* 
> *Kandi, Hyderabad, Telangana - 502285* *Ph.No 6383836804, 8300150807*
> 
> --
> 
> 
> Disclaimer:- The information contained in this electronic message and 
> any attachments to this message are intended for the exclusive use of 
> the
> addressee(s) and may contain proprietary, confidential or privileged 
> information. If you are not the intended recipient, you should not 
> disseminate, distribute or copy this email. Please notify the sender 
> immediately and destroy all copies of this message and any 
> attachments. The views expressed in this E-mail message (including the 
> enclosure/(s) or
> attachment/(s) if any) are those of the individual sender, except 
> where the sender expressly, and with authority, states them to be the 
> views of IIT Hyderabad. Before opening any mail and attachments please 
> check them for viruses, malware, and the sender email address is indeed
from IITH domain.
> IITH does not accept any liability for malware infected mails.
> 
> <nowaterbox.png><waterbox.png>________________________________________
> _______
> AMBER mailing list
> AMBER.ambermd.org<mailto: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, 2 Dec 2020 17:04:52 +0700
From: lomzov <lomzov.niboch.nsc.ru>
Subject: Re: [AMBER] Imaging issue in DNA - cpptraj
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <715304c9-aa30-5df4-9098-331ebef82aa0.niboch.nsc.ru>
Content-Type: text/plain; charset=windows-1252; format=flowed
Hi,
We were not successful to unwrap DNA duplexes using cpptraj.
To solve this problem at the modeling stage, we found two solutions:
1) as suggested by Anselm using iwrap = 0, but for long-term simulations
(more than 50-100 ns) water molecules and cations may go too far and this
cannot be written to the old format mdcrd file.
To solve this issue you can simulate with iwrap = 0 for 50 ns, and than
short simulate iwrap = 1 for 5-10 ns.
Sometimes it helps.
2) use very weak Cartesian restraints (0.01 kcal / mol / A) for two atoms in
opposite chains with iwrap = 1. For example, for 16 bp duplex
   ntr = 1,
   restraint_wt=0.01 ,
   restraintmask=" :8,24.C4'",
This does not allow translation movement of the duplex, but becaose of low
value of restraint does not change duplex conformation.
If you want to analyze conformation changes, you could restart simulation
every few nanoseconds (5-10 ns) using the reference file, which was obtained
at previous stage
stage 1: ..... -r 1.restrt -ref 0.inpcrs stage 2: ..... -r 2.restrt -ref
1.restrt stage 3: ..... -r 3.restrt -ref 2.restrt
good luck!
Alex
On 02.12.2020 16:23, Dr. Anselm Horn wrote:
> Hi,
>
> just to add a comment:
> If you used iwrap=1 in your simulation input, try to use the unwrap 
> command in cpptraj, expecially, if you are not interested in the 
> solvent
> molecules: strip off these first, the do the unwrap and omit the 
> (auto)image commands.
>
> However, you may want to use a rms fit command to obtain a trajectory 
> better to visualize.
>
> Regards,
>
> Anselm
>
>
> On 12/02/2020 09:12 AM, Gustaf Olsson wrote:
>> Short of increasing the solvent buffer to avoid jumps, trying to play
around with the masks for image/autoimage seems reasonable.
>>
>> See what happens if you autoimage with a mask defined. Either trying to
center the entire DNA or as suggested
(https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small
region of the DNA which should be close to the center of the box.
>>
>> Best regards
>> // Gustaf
>>
>>
>> On 2 Dec 2020, at 08:17, Satyaseelan C
<bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote:
>>
>> Dear Amber users,
>>                I am facing an imaging issue during the MD simulation 
>> of a DNA duplex. Due to this, the RMSD is shooting up and falls back 
>> during the middle of the simulation. I am observing this problem for 
>> 50ns during the simulation. I used autoimage option followed by image
option as below:
>>
>> parm prmtop
>> trajin trajin.nc
>> autoimage
>> center :1-16 origin
>> image origin center familiar
>> center :1-32 origin
>> image origin center familiar
>> trajout reimage.nc
>> go
>>
>> When I don't apply any imaging, the DNA strands are separated and 
>> going out of the box in some frames. But, after performing imaging, 
>> the problem is not completely resolved. Here, a stretch of DNA strand 
>> is going away and causes distortions in the structure for 50ns. I 
>> have attached the corresponding snapshots.
>>
>> Please suggest any alternative options to overcome this issue.
>>
>>
>> Thanks in advance
>> Sathyaseelan
>>
>> --
>> *Thanks & Regards*
>>
>> *C .Sathyaseelan *
>> *PhD Research Scholar*
>> *C/o Dr. Thenmalarchelvi Rathinavelan* *Molecular Biophysics Lab* 
>> *Dept. of Biotechnology* *Indian Institute of Technology (IIT)* 
>> *Kandi, Hyderabad, Telangana - 502285* *Ph.No 6383836804, 8300150807*
>>
>> --
>>
>>
>> Disclaimer:- The information contained in this electronic message and 
>> any attachments to this message are intended for the exclusive use of 
>> the
>> addressee(s) and may contain proprietary, confidential or privileged 
>> information. If you are not the intended recipient, you should not 
>> disseminate, distribute or copy this email. Please notify the sender 
>> immediately and destroy all copies of this message and any 
>> attachments. The views expressed in this E-mail message (including 
>> the enclosure/(s) or
>> attachment/(s) if any) are those of the individual sender, except 
>> where the sender expressly, and with authority, states them to be the 
>> views of IIT Hyderabad. Before opening any mail and attachments 
>> please check them for viruses, malware, and the sender email address is
indeed from IITH domain.
>> IITH does not accept any liability for malware infected mails.
>>
>> <nowaterbox.png><waterbox.png>_______________________________________
>> ________
>> AMBER mailing list
>> AMBER.ambermd.org<mailto: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: 11
Date: Wed, 2 Dec 2020 13:27:56 +0100
From: Pavl?na Pokorn? <pokorna.pavlina.ibp.cz>
Subject: Re: [AMBER] NOE analysis with cpptraj
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CACHm3M0XvrVPxXxh598wNgiSbZSjSwqWGP1We9uK19n_CaNAkA.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Daniel,
thanks for Your reply. No, I don't want cpptraj to use closer of the two (or
more) distances but to use their r^-6 weighted average. i.e.: to use
r^-6 weighted average of all distances per frame in the mask to compute
their final r^-6 weighted average over the whole trajectory to get NOE
violations. What I get now is r^-6 weighted average over the whole
trajectory computed for center-of-mass distances, not for r^-6 weighted
averages (per frame). This leads to slightly higher values of NOE violations
for multiple-mask distances with "distance type noe" than what is the
correct value. Sander can be also used to analyze NOE violations and there
the r^-6 weighted averaging for multiple-atom NOEs works well.
Best wishes,
Pavlina
On Wed, Nov 25, 2020 at 4:26 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Sorry for the long delay on this. So do you mean you want cpptraj to 
> automatically choose the closer of the two distances? If so, you can't 
> do that with the 'distance' command, but you might be able to get it 
> to work with the 'nativecontacts' command and the 'mindist' keyword.
> The generated dataset with the [mindist] aspect could then be sent to 
> the 'stat' analysis. Disclaimer: I haven't had a chance to test it, 
> but that seems like it should work with those atom masks.
>
> -Dan
>
> On Mon, Oct 19, 2020 at 9:18 AM Pavl?na Pokorn? 
> <pokorna.pavlina.ibp.cz>
> wrote:
> >
> > Dear all,
> >
> > I have a question regarding NOE analysis when using a multiple-atom 
> > mask with cpptraj.
> >
> > If I use:
> > distance 117RADE_H8-41LYS_QG :117.H8 :41.HG= type noe noe_weak 
> > analyze statistics all out noe.dat noeout noeout.dat
> >
> > --> cpptraj then uses center-of-mass of :41.HG2 and :41.HG3 atoms to
> > compute its r6 weighted average distance with :117.H8 instead of
> treating
> > each of the :41.HG* atoms individually. There is no problem if I
> calculate
> > NOE with equivalent command using masks which both contain only one 
> > hydrogen atom.
> >
> > So, is it possible to make cpptraj use the r6 weighted averaging 
> > instead
> of
> > center-of-mass averaging when "type noe" is specified for distance 
> > action with multiple atoms in the mask? Did I miss something with my 
> > cpptraj commands?
> >
> > Thank You,
> > Pavlina Pokorna
> >
> >
> > --
> > RNDr. Pavl?na Pokorn?
> > *PhD student*
> > Institute of Biophysics of the CAS, v. v. i.
> > Kralovopolska 135, 612 65 Brno
> > _______________________________________________
> > 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
>
--
*RNDr. Pavl?na Pokorn?*
*PhD student*
Institute of Biophysics of the CAS, v. v. i.
Kralovopolska 135, 612 65 Brno
------------------------------
Message: 12
Date: Wed, 2 Dec 2020 08:51:08 -0500
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<20201202135108.br5y4ktxpfpbfxib.Davids-MBP.fios-router.home>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Wed, Dec 02, 2020, Karl Kirschner wrote:
>
>impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
One point is this: the command above doesn't specific which atoms are to
be *moved* in order to  make the dihderal be 120 degrees.  Should the
program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
to it)?  Or do something else?  This may not be important in some
workflows, but can be key in others.
The pyMol example has the same problem.  Of course, its
documentation may be better in explaining what choices are made.
These sorts of manipulations are a natural for NAB (aka "molecular
awk"), but it has its own learning curve and documentation deficiencies.
....dac
------------------------------
Message: 13
Date: Wed, 2 Dec 2020 08:55:09 -0500
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Imaging issue in DNA - cpptraj
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<20201202135509.ndw6p5uz7zh6dqyq.Davids-MBP.fios-router.home>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Wed, Dec 02, 2020, lomzov wrote:
>1) as suggested by Anselm using iwrap = 0, but for long-term simulations
>(more than 50-100 ns) water molecules and cations may go too far and
>this cannot be written to the old format mdcrd file.
The expectation is that you will use netcdf format for trajectory and
restart files.  If you need the old format mdcrd for something, then
do this in cpptraj:
      read in the netcdf trajectory
      image the water ions
      write out the trajectory in mdcrd format
...good luck...dac
------------------------------
Message: 14
Date: Wed, 2 Dec 2020 14:03:54 +0000
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	
<DM5PR02MB2715829462FF2DCEF9E521B1DCF30.DM5PR02MB2715.namprd02.prod.outlook.
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Thank you for the help in this.
In a protein the phi and psi angles require 2 adjacent
residues.  Calculating these angles and rotating is
fairly easy.  It is a matter of what is rotated to agree
to a PDB model starting from a linear backbone model.
I will be working the angle rotations further in tleap today,
a little delayed at the moment.
In principle, you should rotate the entire peptide chain
after or before the ith residue as these are bonded in
%% phi  C(i-1)-N-CA-C
%% psi N-CA-C-N(i+1)
The actual rotation angle about the intermediary N-CA
or CA-C axis should be the dihedral angle geometrically.
Maybe my own Matlab algorithms aren't correct yet, but
I have checked this many times.  I will try to use tleap or
cpptraj instead as a check.
Gordon Chalmers
Department of Computer Science
Complex Carbohydrate Research Center
University of Georgia
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, December 2, 2020 8:51 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
On Wed, Dec 02, 2020, Karl Kirschner wrote:
>
>impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
One point is this: the command above doesn't specific which atoms are to
be *moved* in order to  make the dihderal be 120 degrees.  Should the
program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
to it)?  Or do something else?  This may not be important in some
workflows, but can be key in others.
The pyMol example has the same problem.  Of course, its
documentation may be better in explaining what choices are made.
These sorts of manipulations are a natural for NAB (aka "molecular
awk"), but it has its own learning curve and documentation deficiencies.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 15
Date: Wed, 2 Dec 2020 14:03:51 +0000
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	
<DM5PR02MB2715D20E3D3F3E02D24DE6F2DCF30.DM5PR02MB2715.namprd02.prod.outlook.
com>
	
Content-Type: text/plain; charset="us-ascii"
Thank you for the help in this.
In a protein the phi and psi angles require 2 adjacent
residues.  Calculating these angles and rotating is
fairly easy.  It is a matter of what is rotated to agree
to a PDB model starting from a linear backbone model.
I will be working the angle rotations further in tleap today,
a little delayed at the moment.
In principle, you should rotate the entire peptide chain
after or before the ith residue as these are bonded in
%% phi  C(i-1)-N-CA-C
%% psi N-CA-C-N(i+1)
The actual rotation angle about the intermediary N-CA
or CA-C axis should be the dihedral angle geometrically.
Maybe my own Matlab algorithms aren't correct yet, but
I have checked this many times.  I will try to use tleap or
cpptraj instead as a check.
Gordon Chalmers
Department of Computer Science
Complex Carbohydrate Research Center
University of Georgia
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, December 2, 2020 8:51 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
On Wed, Dec 02, 2020, Karl Kirschner wrote:
>
>impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
One point is this: the command above doesn't specific which atoms are to
be *moved* in order to  make the dihderal be 120 degrees.  Should the
program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
to it)?  Or do something else?  This may not be important in some
workflows, but can be key in others.
The pyMol example has the same problem.  Of course, its
documentation may be better in explaining what choices are made.
These sorts of manipulations are a natural for NAB (aka "molecular
awk"), but it has its own learning curve and documentation deficiencies.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 16
Date: Wed, 2 Dec 2020 14:10:11 +0000
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	
<DM5PR02MB271576BCB52CD93FA422316FDCF30.DM5PR02MB2715.namprd02.prod.outlook.
com>
	
Content-Type: text/plain; charset="us-ascii"
Another point: it is possible to do a search of the
peptide bond angles to find what is being rotated
in order to agree with a PDB model, but this sort of
defeats the purpose of simple linear rotations.
TBD.
Gordon Chalmers
________________________________
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Sent: Wednesday, December 2, 2020 9:03 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
Thank you for the help in this.
In a protein the phi and psi angles require 2 adjacent
residues.  Calculating these angles and rotating is
fairly easy.  It is a matter of what is rotated to agree
to a PDB model starting from a linear backbone model.
I will be working the angle rotations further in tleap today,
a little delayed at the moment.
In principle, you should rotate the entire peptide chain
after or before the ith residue as these are bonded in
%% phi  C(i-1)-N-CA-C
%% psi N-CA-C-N(i+1)
The actual rotation angle about the intermediary N-CA
or CA-C axis should be the dihedral angle geometrically.
Maybe my own Matlab algorithms aren't correct yet, but
I have checked this many times.  I will try to use tleap or
cpptraj instead as a check.
Gordon Chalmers
Department of Computer Science
Complex Carbohydrate Research Center
University of Georgia
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, December 2, 2020 8:51 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] question about dihedral angles
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
On Wed, Dec 02, 2020, Karl Kirschner wrote:
>
>impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
One point is this: the command above doesn't specific which atoms are to
be *moved* in order to  make the dihderal be 120 degrees.  Should the
program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
to it)?  Or do something else?  This may not be important in some
workflows, but can be key in others.
The pyMol example has the same problem.  Of course, its
documentation may be better in explaining what choices are made.
These sorts of manipulations are a natural for NAB (aka "molecular
awk"), but it has its own learning curve and documentation deficiencies.
....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
------------------------------
Message: 17
Date: Wed, 2 Dec 2020 11:50:58 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] question about dihedral angles
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAAC0qOZ6fau_S4hV-7f=bd-8PLdS2AN4864spumxQ+4f6d=FVg.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
The command for calculating dihedral angles in cpptraj is 'dihedral'.
The command for rotating atoms around a dihedral is 'rotatedihedral'.
Both are documented in the manual. The convention in cpptraj is for
all atoms connected to the greater atom index to move; those connected
to the lower atom index are fixed. Cpptraj does the rotation in
Cartesian space - I think tleap may do it via internal coordinates but
I'm not sure about that.
-Dan
On Wed, Dec 2, 2020 at 9:04 AM Gordon Richard Chalmers <gordoncs.uga.edu>
wrote:
>
>
> Thank you for the help in this.
>
> In a protein the phi and psi angles require 2 adjacent
> residues.  Calculating these angles and rotating is
> fairly easy.  It is a matter of what is rotated to agree
> to a PDB model starting from a linear backbone model.
>
> I will be working the angle rotations further in tleap today,
> a little delayed at the moment.
>
> In principle, you should rotate the entire peptide chain
> after or before the ith residue as these are bonded in
>
> %% phi  C(i-1)-N-CA-C
> %% psi N-CA-C-N(i+1)
>
> The actual rotation angle about the intermediary N-CA
> or CA-C axis should be the dihedral angle geometrically.
>
> Maybe my own Matlab algorithms aren't correct yet, but
> I have checked this many times.  I will try to use tleap or
> cpptraj instead as a check.
>
> Gordon Chalmers
> Department of Computer Science
> Complex Carbohydrate Research Center
> University of Georgia
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Wednesday, December 2, 2020 8:51 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] question about dihedral angles
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
>
> On Wed, Dec 02, 2020, Karl Kirschner wrote:
> >
> >impose mymolecule {7} { {C1 C2 C3 C4 120.0} }
>
> One point is this: the command above doesn't specific which atoms are to
> be *moved* in order to  make the dihderal be 120 degrees.  Should the
> program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
> to it)?  Or do something else?  This may not be important in some
> workflows, but can be key in others.
>
> The pyMol example has the same problem.  Of course, its
> documentation may be better in explaining what choices are made.
>
> These sorts of manipulations are a natural for NAB (aka "molecular
> awk"), but it has its own learning curve and documentation deficiencies.
>
> ....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
------------------------------
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