[gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

[Mark Abraham]

On Mon, Nov 18, 2013 at 11:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/18/13 5:05 PM, Hari Pandey wrote:
>
>> Dear Dr. Tsjerk,
>> Many many thanks for your help. This makes me some sense but still I am
>> confused about that you indicated me to look out the gromacs/share
>>  directory.  In my gromacs, I have following directory tree:
>> gromacs/share/gromacs/top
>> I did not found a format. I am wandering what could be that file in which
>> I can check format.
>>
>
> The atommass.dat file is in /gromacs/share/gromacs/top.
>
>
>  Other is, What I am doing my simulation is: pdb2gmx--->editconf.--->genbox---grompp---mdrun.
>>  But to get (.tpr) I need to pass editconf first.
>>
>
> The output from editconf is getting confused based on the atypical
> nomenclature that you are using.  It thinks SOD is S instead of Na.  The
> .top for the system is definitive, as has been stated several times.  The
> .tpr file is built based on the .top and not the atom names.  You can
> convince yourself of the integrity of the system using gmxdump on the
> resulting .tpr file and see the correct masses.
>
>
>  Would you please let me know how do I include mass on (.pdb).
>>
>
> PDB files do not include mass.


... which is the root of the problem. Hari is choosing to name sodium SOD
in his input, and to depend on editconf being able to recognize that this
is sodium. That's a hard problem to solve in general, and editconf has only
a limited set of machinery. Rather than spend time on more powerful
machinery for a tiny use case, there's a warning that you should check
sanity. Looking ahead, most of the force fields will expect sodium atoms
and residues to be named "NA" so Hari should probably go and do that to
save further pain when grompp anxiously warns that the names don't match.
Or use the back of the nearest envelope, rather than editconf -density to
work out how many atoms go in how big a box ;-)

Mark


>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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