[gmx-users] ffgmx2-c.tdb

[Derrick Guang Yuh Lee]

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

	-NH-CH-C(=O)-NH2

instead of like

	-NH-CH-C(=O)-OH

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.



Sincerely

 - 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
catalyst."
                                                              - bruce lee