[gmx-users] Atom X in residue YYY was not found in rtp fil
jalemkul at vt.edu
Sat Feb 27 22:42:38 CET 2016
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
> 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
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.
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
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