[gmx-users] Alternative TRP residue

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 11 18:11:35 CEST 2009

abelius wrote:
> Dear All,
> I have AmberFF parameters for a TRP excited state and I was wondering if 
> it was possible to create an alternative TRP residue for gromacs?
> Things I've done so far:
> * Download and install amber99 for gromacs
> * Add a new residue [ ETRP ] with adapted charges to the amber99.rtp file
> * Add ETRP to aminoacids.dat
> My question is where do I go from here, how can I add distances (bond 
> lengths) and angles?
you can add everything in your amber.rtp file and then rename the 
residue in your pdb to ETRP. That should be all.

> Thank you very much,
> Abel
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se

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