Re: [AMBER] scee=scnb=1

From: Ross Walker <>
Date: Wed, 6 Jul 2011 11:02:12 -0700

Dear Paul,

> I want to simulate a carbohydrate and TMAO in Amber10 for carbohydrate
> i
> use GLYCAM_06 force field and TMAO parameters are taken from kast at
> el.
> >xleap
> >GLYCAM_06 force field
> >TMAO molecule with kast parameters (lib and frcmod)
> >load carbohydrate molecule,
> > solvate TMAO and carbohydrate with water
> >svae the top and crd file
> is this possible to run with scee=scnb=1 in sander for the entier
> system?

In AMBER 10, yes, you just set scee=1.0, scnb=1.0 in the cntrl namelist.
However, you should check what values of SCEE and SCNB were used in the
development of the TMAO parameters. If they were the default of 1.2 and 2.0
respectively then using 1.0 for the whole system will be using the incorrect
parameters for TMAO. This may be fine as long as you believe you can defend
that decision. A better option would probably be to upgrade to AMBER 11 and
AMBERTools 1.5 which will allow you to use mixed SCEE and SCNB values in
your simulation allowing you to use the correct combination in each case.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Wed Jul 06 2011 - 11:30:03 PDT
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