[gmx-users] Re: acetonitrile from amber to gromacs

Alan alanwilter at gmail.com
Wed May 19 23:38:42 CEST 2010

Dear Vedat,

On Wed, May 19, 2010 at 20:36, <gmx-users-request at gromacs.org> wrote:

> @rui
> acpypi -i ch3cn_210.pdb
> says: "cannot find template for residue C3N in our library". and indeed,
> there's no residue C3N in my ffamber99sb.rtp file
> (and i don't know, how to use it in order to generate my topology or even
> an rtp file?!)

Have a bit of patience and try to read a bit more about ACPYPE.

1) Read the info there, I am sure you'll find it useful;
2) You'll learn that you need to have just one molecule in a pdb and not the
whole box if you want the topologi of C3N.
3) It took me 2s to get the topology with acpype but months to write the
code, so if you'd take some few minutes to read and use an updated version
(it's not acpypi anymore BTW)...

BTW, how did you get this message "cannot find template for residue C3N in
our library"?



Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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