[gmx-users] ffgmx2-c.tdb

Ken Rotondi ksr at chemistry.umass.edu
Mon Jul 25 21:50:09 CEST 2005


You don't have to do any of that. Look at the options generated by 
using the -ter (interactive termini selection) flag in pdb2gmx.

Best of luck,


On Jul 25, 2005, at 2:53 PM, Derrick Guang Yuh Lee wrote:

> 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
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