AMBER Archive (2003)

Subject: Re: compatibility of amber with NAMD

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Fri Feb 14 2003 - 08:27:27 CST

Hi,
> I was wondering if anyone has any expertise in trying to use amber
> generated files (topology especially) in NAMD. More specifically, is there
> a way to use the .prmtop file as input for NAMD (so not to transform it
> into a .psf file) if one also uses the amber force field in NAMD?
...it's quite straightforward, just follow the manual.
If you want rigid TIP3P waters,
see
http://structbio.vanderbilt.edu/archives/amber-archive/2003/0130.phtml,
the trick I described there really seems to work.
just be aware that it's an ungodly hack inside an ungodly hack :-)
good luck
Andreas