[gmx-users] adding SR2++ to charm27 force field

[Justin Lemkul]

On 4/15/15 9:11 AM, Ming Tang 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++
>

We need to see the *actual terminal output* to diagnose this.  It would also be 
useful if you can upload a tarball with all input files (coordinates and full 
modified force field directory) to a file-sharing site for a better look. 
Something is inconsistent, but you haven't given us the right information to 
find out what.

-Justin

> 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

==================================================