[gmx-users] Unable to generate .rtp file from gro and pdb file.

Karpurmanjari Kakati ch18resch01002 at iith.ac.in
Mon Nov 5 18:17:06 CET 2018

Dear Justin,

I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the
aminoacids.rtp file . I have all the files of OPLS AA force field in my
working directory.
For that I tried to generate the initial rtp format file from the hydroxy
proline's .pdb and .gro  files using the following command:
gmx x2top  -f hyd.gro  -r hyd.rtp  -pbc -ff oplsaa

and I got the following error:

Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t
There are 23 name to type translations in file oplsaa.ff
Generating bonds from distances...
atom 18
Can not find forcefield for atom CA-2 with 4 bonds
Can not find forcefield for atom C-3 with 3 bonds
Can not find forcefield for atom CD-7 with 4 bonds

Program:     gmx x2top, version 2018.1
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 205)

Fatal error:
Could only find a forcefield type for 15 out of 18 atoms.

Can you help me with this.

I want to add this residue to the rtp file so that I can use the step
pdb2gmx directly.


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