[gmx-users] Unable to make .gro file

Jeffrey Chua chuademon at gmail.com
Fri Jun 3 05:56:45 CEST 2005

Dear Friends,

Hi! Im Jeff Chua, a new user to gromacs... I've been trying to do a md run
on a dimer of beta carrageenan but whenever i try to produce a .gro and a
.top file out of the given pdb file (using pdb2gmx_d since I dont have
the pdb2gmx) the following error message is given.

Processing chain 1 (80 atoms, 34 residues)
Opening library file /home/apps/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 18 acceptors
There are 0 hydrogen bonds
Fatal error: Residue 'CT' not found in residue topology database

[jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample Runs,11:39]$

Looking at the produced files, I see that a .top file has been produced
and it contains the following:

[jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample Runs,11:42]$ ls
#beta.top.1#  BetaDimer.pdb  KappaDimer.pdb  beta.top
[jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample Runs,11:42]$ cat
;       File 'beta.top' was generated
;       By user: jchua (733)
;       On host: ahpc
;       At date: Fri Jun  3 11:39:18 2005
;       This is your topology file
;       80   61
; Include forcefield parameters
#include "ffoplsaa.itp"

[jchua,/usr/ahpc-data-2/home/jchua/gromacs/Sample Runs,11:42]$

Ive looked over the oplsaa files that comes with gromacs and it does
contain CT atom types. Am I doing something wrong?? Im attaching also the
pdb file for your reference on the matter. (I hope this doesnt flood your
emails...if it does, I apologize)

I hope you could help me on this... thank you and God Bless.


Jeff Chua
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