[gmx-users] analysing charmm trajectories

[Chiara Parravicini]

Dear Justin,

I removed the cmap tems form the .top file as you suggested and the problem
is now solved.
Thanks a lot for your precious help.

Chiara

2015-01-14 0:42 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 1/13/15 8:18 AM, Chiara Parravicini wrote:
>
>> Dear all,
>>
>> I'd like to use the gromacs analysis tool to analyse a simulation
>> performed
>> with charmm.
>> I installed the latest gromacs version (5.0.4), in which both .dcd
>> trajectories and all the files read also by vmd should be readable. After
>> that, the trajectory is correctly processed by gromacs, but I've troubles
>> with the analysis tools that need .tpr files.
>> As suggested in some previous posts, I've generated a fake file .top with
>> vmd, useful to produce a new .tpr suitable for the analysis. I also
>> installed the charmm36 forcefield in the gmx top directory (the same that
>> I
>> used in the simulation).
>> When I use grompp to generate a .tpr, I get this error:
>>
>> Fatal error:
>> Unknown cmap torsion between atoms 5 7 9 22 24
>>
>> Among the possible solutions I found the use of this patch, but this was
>> concerning an older vs of gromacs: “0001-Fix-pdb2gmx-merge-cmap.patch”,
>> so
>> I skipped it during installation.
>>
>> I do not understand if this error it's a matter of forcefield or it
>> depends
>> on something else. Does anyone could help me to figure-out the origin of
>> the error and how to fix the problem?
>>
>> Also pdb2gmx is not working because some atoms are not found in the
>> forcefield (such as CAY, used by charmm for methylated methionine).
>> Manipulating the forcefield would fix both the problems? In this case how
>> should I proceed?
>>
>> I'd really appreciate any suggestion!
>>
>>
> So the .top that VMD wrote is probably wrong in some way, but if you're
> just using it to do analysis and not actually run a simulation, I'd say you
> can probably remove the offending CMAP term from the .top and proceed.
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>