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

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 8 13:10:57 CEST 2008

Quoting Mattia Sturlese <mattia.sturlese at unipd.it>:

> 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 ....

Be aware that the charges given by PRODRG are often unsatisfactory, and usually
(if not always) require refining.

> 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 ?

Use the other entries in the .rtp file as a guide.  Bonded parameters are found
in ffG43a1bon.itp.


> Thanks folk!!
> Mattia Sturlese
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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