[gmx-users] Atom X in residue YYY was not found in rtp fil

[Justin Lemkul]

On 2/27/16 4:38 PM, Dawid das wrote:
> Dear Gromacs Experts,
>
> I have created a new residue for which atom names in my *.pdb file are
> 4-signs long.
> When I run gmx pdb2gmx I get following error
>
> Fatal error:
> Atom MCA in residue CH6 65 was not found in rtp entry CH6 with 33 atoms
> while sorting atoms.
>
> I am absolutely one hundred percent sure that I did not define atom called
> MCA.
> There are atoms such as MCA1, MCA2, etc. in my *.rtp and other relevant
> files. I think that the issue is related to the fact that in my *.pdb file,
> the atom name
> is now "glued" to residue name:
>
> ATOM    478  N      CH6 A  65      11.385  68.446 -10.896 1.00
> 15.50           N
> ATOM    479  MCA1CH6 A  65     10.237  67.920 -10.172 1.00 14.40           C
> ATOM    480  MC1  CH6 A  65       9.431  69.147  -9.749  1.00
> 15.10           C
>
> This is part of my *.pdb file. I know that it should not be a problem,
> because *.pdb
> files are read by positions, like *.gro files, but I cannot see any other
> explanation.
>

Content is read by position, which is precisely your problem.

Your atom name is in incorrect alignment. Columns 13-16 are for the name. Column 
17 is for the alternate location indicator. Since you have "MCA" in positions 
14-16, this is all pdb2gmx reads, since "1" is in position 17.

http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM

-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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