Hi David,
> Thanks Jason. I guess I'll have to manually go through the file and
> find the
> charges and parameters of the molecules I'm looking for.
Be aware that the Charmm force field and the Amber force field are NOT
directly compatible. You cannot simply copy parameters from one to the
other. For example, Charmm typically uses Urey Bradley and CMAP terms which
are not in the standard AMBER equation. Additionally the combining rules for
the VDW are different and 1-4 nonbond interactions are scaled differently.
Thus one cannot simply mix AMBER and CHARMM force fields within the same
simulation. You can certainly do it but the results will be difficult to
defend the validity of.
In your case I suggest setting up your entire system using the charmm force
field and writing a psf and crd file for the entire system. You can then
convert this through chamber and run it in AMBER which will then run your
simulation using the charmm force field as you defined in the psf.
Good luck,
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Wed Jul 27 2011 - 10:30:02 PDT
