[gmx-users] pdb2gmx warning residue mapping

[Justin Lemkul]

On 7/1/15 2:13 PM, Nikhil wrote:
> Dear all,
> when i run pdb2gmx -f name.pdb with charmm27 and tip3 water model for my
> structure i got an warning:
>   Residue 1 named GLN of a molecule in the input file was mapped to an
> entry in the topology database,but the atom CA used in that entry is not
> found in the input file.Perhaps your atom and reside naming needs to be
> fixed.
>
> when i  checked my structure for four or five times i couldnt find any
> problem atom CA which is defined in charmm27 still why this error.
>
> how to solve this error or if i avoid and proceed it will make problem
> during minimization and md?
>
> here is GLN entry
> ATOM   42   CD2  LEU A   6      -7.733  -2.176   0.996  1.00  0.00
> C
> ATOM   43   CA   GLN A   1      -3.232   3.298  -0.224  1.00  0.00
> C
> ATOM   44   CB   GLN A   1      -4.479   3.910   0.508  1.00  0.00
> C
> ATOM   45   CG   GLN A   1      -4.699   5.392   0.155  1.00  0.00
> C
> ATOM   46   CD   GLN A   1      -6.125   5.743   0.501  1.00  0.00
> C
> ATOM   47   NZ   GLN A   1      -6.625   7.021   0.232  1.00  0.00
> N
> ATOM   48   OD   GLN A   1      -6.886   4.863   0.922  1.00  0.00
> O
> ATOM   49   HN   GLN A   1      -2.342   1.326   0.325  1.00  0.00
> H
> ATOM   50   HN   LEU A   2      -1.012   3.459  -1.579  1.00  0.00
> H
> ATOM   51   HN   LYS A   3       0.953   2.002  -0.768  1.00  0.00
> H
> ATOM   52   HN   ALA A   4       1.202  -0.067  -0.562  1.00  0.00
> H
> ATOM   53   HN   LEU A   6      -2.606  -0.728   0.937  1.00  0.00
> H
> ATOM   54   HN   LYS A   5      -0.672  -1.114   0.652  1.00  0.00
> H
> ATOM   55   HA   LEU A   2       0.683   5.077  -1.474  1.00  0.00
> H
>

You're missing all kinds of atoms.  This coordinate file is pretty hopeless.

-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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