[gmx-users] topology file for small organic molecule

David spoel at xray.bmc.uu.se
Sat Sep 25 10:31:22 CEST 2004

On Sat, 2004-09-25 at 02:00, Yunfeng Hu wrote:
> Hi, I am trying to build a topology file for an antibody substrate 
> using pdb2gmx -f test.pdb -p test.top -o test.gro. I got the following 
> error. Why does the program complain about the residue name since I am 
> using OPLS for small molecule only. Thanks.

The error message is clear:

Fatal error: Residue 'XXX' not found in residue topology database

You will have to do it manually (for OPLS) or use prodrg for gromos force fields.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list