[gmx-users] topology file for small organic molecule

[David]

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.
________________________________________________________________________
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
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