[gmx-users] ffgmx2-c.tdb

Derrick Guang Yuh Lee k24dgyl at mun.ca
Mon Jul 25 20:53:43 CEST 2005

Dear GMX-Users,

I am attempting to generate a .top and .itp file for a peptide I have
using pdb2gmx and the ffgmx2 forcefields. When I run pdb2gmx, I get:

Fatal error: atom C not found in residue 19NH2 while combining tdb and rtp

I understand that this is happening because one of the residues in the
peptide is setup like


instead of like


So right now I am attempting to edit the ffgmx2-c.tdb file to add in this
particular bond, but I am not exactly sure how it works. Can anyone give
me a hand or some insight into the appropriate modifications I need to do
in order to create my forcefields. Thanks.


 - Derrick Lee

 Derrick Guang Yuh Lee
 Department of Mathematics and Statistics / Department of Biochemistry
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
                                                              - bruce lee

More information about the gromacs.org_gmx-users mailing list