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

[Justin Lemkul]

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.

-Justin

-- 
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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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