[gmx-developers] Caps of the Peptide

[David]

On Wed, 2003-09-17 at 22:19, Abhishek Jha wrote:
> Dear List,
>  I am trying to switch to use gmx and the first problem I ran into was
> capping my peptide. I can see NME (or NAC) in the aminoacids.dat file and
> as well as in ff*.rtp but the pdb2gmx fails to recognize it. Any
> suggestion and help will be appreciated.
this is actually a gmx-users question but anyway...

do you have the same residue name in the pdb file as you have 
in the databases?

The caps do not necessarily exist in every force field, although they
can quite easily be generated (read added manually)
> 
> Regards,
> Abhishek
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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