Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Wed, 07 May 2014 17:10:38 +0200

Hi,

You need to create a new force field library for Glycine; the Glycine
form is related to the pH; at pH 7 you have a zwitterion form:
   (+)NH3CH2CO2(-)

You can use http://q4md-forcefieldtools.org/REDServer-Development/ to
generate a force for that molecule; at the end you end up with a
leaprc.q4mdfft file that you load in the LEaP problem (AmberTools)

See http://q4md-forcefieldtools.org/REDServer-Development/images/PyRED.gif
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#6

regards, Francois


> I want to simulate Glycine in vacuum with amber,what I done like this:
>
> tleap ?s ?f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> a = sequence{GLY}
> saveamberparm a gly.prmtop gly.inpcrd
>
> but I found that Gly residue in amber is NH-CH2-CO which reduces a -H and a
> -OH compared with the real Glycine like NH2-CH2-COOH in the shape of solid
> powder , so how can I add these two parts to generate a Glycine complete
> prmtop file?



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 07 2014 - 08:30:05 PDT