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

Justin Lemkul jalemkul at vt.edu
Wed Nov 7 16:05:18 CET 2018

On 11/5/18 12:16 PM, Karpurmanjari Kakati wrote:
> 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.

You don't need x2top. Just make a copy of the PRO residue to something 
like HYP and modify it accordingly. You're doing a lot of extra work 
trying to get a functional .n2t file for a straightforward modification 
of an existing residue. You must already know the atom types and charges 
if you're trying to put them in an .n2t file, so cut out the middleman 
and just do it directly.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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