Re: looking for topology and parameters of methamphetamine

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Sun May 09 2010 - 12:42:37 CDT

look for what parameters are missing..NAMD gives error like: CT1 NH1 CT2 CT3
dihedral missing or improper missing or angle or bond missing...look into
"par_all22_...cmap.inp" for closest available parameters..you can also
download latest CHARMM parameters and see if any other molecule has closest
parameters defined for whatever is missing...and add them into your
parameters file or you can make a new parameters file of your own and have
it included in NAMD .conf file with multiple "parameters command"...if you
find nothing closest, one way is to develop them from scratch...see PARATOOL
plugin in VMD ..you can also try...parametrization tutorial of
NAMD......hope it helps..

-harish

On Sun, May 9, 2010 at 9:47 AM, Liao Chen <Liao.Chen_at_utsa.edu> wrote:

> Hi there! I'm looking for psf or topology-parameter files
> of methamphetamine. I tried to make a topology file from "RESI PHE". It
> produced a psf file but some parameters are missing when running NAMD. Your
> help will be appreciated. Liao
>
> Liao Y. Chen, PhD University of Texas at San Antonio One UTSA Circle San
> Antonio, Texas 78249 (210)458-5457 (210)458-4919 Fax Liao.Chen_at_utsa.edu
>

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