[gmx-users] Problem in .gro file

[Justin Lemkul]

On 7/8/15 2:00 PM, faride badalkhani wrote:
> Hi,
>
> I have shared the files via Dropbox
>
> https://www.dropbox.com/sh/bp3d1ugn233domy/AACSSs8fFCmXn_MBRjZBheoda?dl=0
>

You can't repeat atom names within a residue.  This:

HETATM    1  CA  AMC A   1      -9.327  -1.032  -2.562                       C
HETATM    2  HC  AMC A   1     -10.101  -1.364  -3.324                       H
HETATM    3  HC  AMC A   1      -8.844  -0.232  -3.007                       H
HETATM    4  CA  AMC A   1      -8.327  -2.174  -2.335                       C
HETATM    5  HC  AMC A   1      -8.850  -3.081  -2.383                       H
HETATM    6  HC  AMC A   1      -7.952  -2.132  -1.306                       H
HETATM    7  N2  AMC A   1      -9.932  -0.563  -1.272                       N
HETATM    8  N2  AMC A   1      -7.129  -2.164  -3.281                       N

gets turned into:

     1AMC     CA    1  -0.933  -0.103  -0.256
     1AMC     HC    2  -1.010  -0.136  -0.332
     1AMC     N2    3  -0.993  -0.056  -0.127

because pdb2gmx cleans up duplicate atoms.  You went from 1124 atoms in the PDB 
file to 423 in the GRO 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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