[gmx-users] pdb2gmx error

Sneha Menon sneha.menon15 at gmail.com
Tue Apr 7 13:53:30 CEST 2015

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 :

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?

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