[gmx-users] pdb2gmx error

Justin Lemkul jalemkul at vt.edu
Tue Apr 7 14:25:08 CEST 2015

On 4/7/15 7:53 AM, Sneha Menon wrote:
> Dear all,
> I want to simulate a polymer - triphenylphosphine connected to a
> polyethylene glycol polymer using the CHARMM36  forcefield. I obtained the
> parameters of this polymer (resname TPP) using SwissParam. I added this
> molecule to the forcefield by following all the steps mentioned in :
> http://www.gromacs.org/Documentation/Hotos/Adding_a_Residue_to_a_Force_Field
> I want to embed this polymer into a lipid bilayer. I first tried to make a
> topology file for the polymer using :
> *pdb2gmx -f file.pdb -o file.gro*
> However, it showed up the following error:
> Fatal error:
> Residue 1 named TPP of a molecule in the input file was mapped
> to an entry in the topology database, but the atom 16 used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
> I compared the .rtp file as well as the input .pdb file for any missing
> atoms. I could not find any atoms missing or discrepancy in the
> atom/residue naming. What else could be the problem?

You need to provide the relevant snippets of the .rtp and .pdb files.  Something 
is missing or mismatched, otherwise pdb2gmx would not complain.



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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