[gmx-users] dna-protein complex simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Sep 19 09:53:11 CEST 2008

Hi Prasun,

You probably weren't careful enough when changing the residue names.
It seems the residue names need to be shifted by one position, and
pdb2gmx reads DTHY as TH somehow, matching it to THF based on the
first letters.

The proper sed command for the conversion is:

sed -e '{s/\(^.\{17\}\) DG /\1DGUA/; s/\(^.\{17\}\) DA /\1DADE/;
s/\(^.\{17\}\) DC /\1DCYT/; s/\(^.\{17\}\) DT /\1DTHY/}'

Hope it helps,


On 9/19/08, prasun kumar <prasun30 at gmail.com> wrote:
> Dear users,
> I am trying to run a simulation of SNA-protein complex.
> I have changed DA,DC,DT,DG to DADE,DCYT,DTHY,DGUA and all ' to *.
> while running the PDB2GMX command, I am getting following error
> Program pdb2gmx, VERSION 3.3.2
> Source code file: pdb2gmx.c, line: 421
> Fatal error:
> Atom P in residue THF 2 not found in rtp entry with 39 atoms
>              while sorting atoms
> but THF 2 atom is not present in my pdb file.How can I remove this error?
> Thanx in advance
> --
> _______________________________________________
>  gmx-users mailing list    gmx-users at gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the
>  www interface or send it to gmx-users-request at gromacs.org.
>  Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list