[gmx-users] adding SR2++ to charm27 force field
Ming Tang
m21.tang at qut.edu.au
Fri Apr 17 03:30:52 CEST 2015
Hi, Justin
I changed "CL" in my pdb file into "CLA". It can be add ions to equilibrate the charge of the system using the modified charmm27.ff. however, when minimising it, I came across an error like this:
Command line:
mdrun -s em.tpr -deffnm em -v
Back Off! I just backed up em.log to ./#em.log.1#
Reading file em.tpr, VERSION 5.0.4 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
Back Off! I just backed up em.trr to ./#em.trr.1#
Back Off! I just backed up em.edr to ./#em.edr.1#
Low-Memory BFGS Minimizer:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 50000
Using 10 BFGS correction steps.
F-max = inf on atom 30262
F-Norm = -nan
Segmentation fault (core dumped)
tm at tm-HP-Z420-Workstation:~/bmp2$
I searched the mailing list, and found that you said that there is something catastrophically wrong with the input structure. But, it can be minimised using the original charm27 force field in Gromacs when I consider the ion as MG and CAL.
Does this mean that there is something wrong with my modified charmm27.ff?
Thanks.
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Ming Tang
Sent: Friday, 17 April 2015 9:49 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] adding SR2++ to charm27 force field
Hi, Justin
> Hi, Justin
> Thank you so much. I should be much more cautious in the future.
> there is another interesting thing. why doesn't it give the warning regarding mismatching between CLA and CL when I use MG in the pdb and topol file?
There is no connection between the force field and this issue. I can offer no explanation other than to tell you something else is going on there that you didn't account for.
>when using the modified force field, it gives the same warning if I use MG in the pdb and topol file. But, if I use the original force field when considering MG, it does not give the warning regarding mismatching between CLA and CL.
> I did not copy CN88. actually, I typed it. I got those 2 parameters from oplsaa. I found that in ffnanonbonded.itp in charmm27.ff, MG and CAL in different types of pairs has the same sigma1-4 and epsilon 1-4, so I give SR the same as well.
>
Don't mix and match force fields. This is fundamentally unsound. Specific pair interactions (1-4) or nonbonded interactions (NBFIX) are highly tuned for specific interactions. Don't make any assumptions based on things that "look similar."
-Justin
Then, how can I get those parameters?
Thanks.
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Thursday, 16 April 2015 10:13 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] adding SR2++ to charm27 force field
On 4/16/15 12:46 AM, Ming Tang wrote:
> Dear Mark and Justin,
>
> Hi, Justin, I share the files in the dropbox to you. Thanks.
>
Your problem is in ffnonbonded.itp:
Sr 38 87.62000 2.000 A 0.310269 0.494658
"SR" and "Sr" are not the same.
You also have more problems that come from typos:
CN88 SR 1 0.310269 0.494658
There is no such thing as "CN88" - you copied the atomtype wrong (it's CN8B, which makes me wonder where you got these parameters if you're trying to use a non-existent atom type...)
You've got other issues with mismatching names, but those are straightforward to sort out.
-Justin
> Here is the output:
>
> tm at tm-HP-Z420-Workstation:~/bmp2$ grompp -f ions.mdp -c pb.pdb -p topol.top -o ions.tpr
> GROMACS: gmx grompp, VERSION 5.0.4
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at Uppsala
> University, Stockholm University and the Royal Institute of
> Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License as published
> by the Free Software Foundation; either version 2.1 of the License, or
> (at your option) any later version.
>
> GROMACS: gmx grompp, VERSION 5.0.4
> Executable: /your/installation/prefix/here/bin/gmx
> Library dir: /your/installation/prefix/here/share/gromacs/top
> Command line:
> grompp -f ions.mdp -c pb.pdb -p topol.top -o ions.tpr
>
> Setting the LD random seed to 3059859697
>
> -------------------------------------------------------
> Program grompp, VERSION 5.0.4
> Source code file:
> /home/tm/Downloads/gromacs/src/gromacs/gmxpreprocess/toppush.c, line:
> 1019
>
> Fatal error:
> Atomtype SR not found
> For more information and tips for troubleshooting, please check the
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> tm at tm-HP-Z420-Workstation:~/bmp2$
>
>
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
> Of Mark Abraham
> Sent: Thursday, 16 April 2015 1:50 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] adding SR2++ to charm27 force field
>
> I asked to see the output. You can't be helped without someone seeing that.
>
> Mark
> On 15/04/2015 3:12 pm, "Ming Tang" <m21.tang at qut.edu.au> wrote:
>
>> Hi Mark，
>>
>> pdb2gmx doesn't work， and it reminds the same error. Topol file was
>> simply modified by mean from the topol file generated when
>> considering
>> MG2++
>>
>> Thanks
>>
>> Sent from my Huawei Mobile
>>
>> Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Thanks. What is the whole pdb2gmx terminal output?
>>
>> Mark
>>
>> On Wed, Apr 15, 2015 at 3:05 AM, Ming Tang <m21.tang at qut.edu.au> wrote:
>>
>>> Dear Justin and mark,
>>>
>>> I modified the files like this:
>>>
>>> aminoacids.rtp
>>>
>>> [ MG ]
>>> [ atoms ]
>>> MG MG 2.00 0
>>> [ SR ]
>>> [ atoms ]
>>> SR SR 2.00 0
>>>
>>> ions.itp
>>>
>>> [ moleculetype ]
>>> ; molname nrexcl
>>> MG 1
>>>
>>> [ atoms ]
>>> ; id at type res nr residu name at name cg nr charge
>>> 1 MG 1 MG MG 1 2
>>>
>>> [ moleculetype ]
>>> ; molname nrexcl
>>> SR 1
>>>
>>> [ atoms ]
>>> ; id at type res nr residu name at name cg nr charge
>>> 1 SR 1 SR SR 1 2
>>>
>>> ffnonbonded.itp
>>>
>>> CP1 MG 1 0.274842254546 0.051243325419
>>> CP1 SR 1 0.310269 0.494658
>>> whenever there is MG, I add SR.
>>>
>>> ffnanonbonded.itp
>>>
>>> CN7 MG 1 0.274842254546 0.051243325419
>>> CN7 SR 1 0.310269 0.494658
>>> whenever there is MG, I add SR.
>>>
>>> atomtypes.atp
>>>
>>> MG 24.305000 ; Magnesium Ion
>>> SR 87.62000 ; Strontium Ion
>>>
>>> When I copy the modified force field to the working directory, the
>>> PDB file used to consider MG Cannot be minimised too, which works
>>> well with
>> the
>>> original Charmm27 force field. It reminds that atomtype SR not found
>> again.
>>> I use ready-made pdb file and topol file for minimization.
>>>
>>> thanks
>>>
>>> -----Original Message-----
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
>>> Justin Lemkul
>>> Sent: Wednesday, 15 April 2015 1:22 AM
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] adding SR2++ to charm27 force field
>>>
>>>
>>>
>>> On 4/14/15 5:12 AM, Ming Tang wrote:
>>>> Hi Mark,
>>>>
>>>> Thanks for your reply. I am sure as I changed the files in the
>>> charmm27.ff installed in my unbuntu system. Is there any other
>>> things I need to consider?
>>>>
>>>
>>> The files you listed are the only ones that should need to be modified.
>>> Either you missed a step and think you did something you didn't, or
>>> your changes didn't actually take effect (modifying the top-level
>>> installation usually requires admin privileges, so if you tried to
>>> modify without sudo or root it won't take).
>>> Experiment with a local copy of the directory rather than
>>> potentially messing up something system-wide. The error points most
>>> likely to the
>> .atp
>>> file.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences School of Pharmacy Health
>>> Sciences Facility II, Room 629 University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
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