[gmx-users] AA not present in the ffG43a1.rtp

Kukol, Andreas a.kukol at herts.ac.uk
Tue Apr 8 13:11:56 CEST 2008

You find those definitions in ffG43a1bon.itp. As far as I know, they are simply placeholders for the explicit data. Probably you can insert the explicit data into the rtp file.


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Mattia Sturlese
> Sent: 08 April 2008 11:54
> To: gmx-users at gromacs.org
> Subject: [gmx-users] AA not present in the ffG43a1.rtp
> Dear all,
>      I have a protein with an oxidated Cys( to sulfinic acid) , this
> residue is not present in the residue database. I use PRODGR to obtain
> the .itp file of  the residue but I don't start grompp ....
> How I insert this residue in the rtp file?? I trying  insert the
> parameters manually but I have explicit data of angles, bond, dihedral
> and impropers....but ffG43a use Gromos Type definition as ga_XX or
> gb_XX......  Where i find a database of this gromos type? Or How I can
> insert my .itp file ?
> Thanks folk!!
> Mattia Sturlese
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