Hi,
> I used MOE (chemical computing group) to save docked complex which is used
> to prepare prmtop and inpcrd file. From MOE, I saved ligands as mol2 file
> which were used to make frcmod file and ligand library(LIG.lib). Can we
> compare the charges in ligand library (LIG.lib) and those in ligand.mol2
> ?.
> Should they be same for every atom ?
That depends. Did you use the mol2 file as a starting point to build your
own lib file with new charges and parameters? Then the charges will
differ. If you just save the mol2 file as a lib, then the charges should
be identical. Note that the lib-format is redundant, you can use your
mol2-file in leap to define the ligand. Using libs doesnt hurt, though.
Be careful to check where the MOE charges come from! In Amber philosophy,
partial charges may mean something different from those in a docking
program. Normally, you would perform a RESP charge fit for your new
molecule to obtain partial charges.
> can we check somewhere whether the charges we applied to ligand are being
> used during simulation ?
You can look into the prmtop file for the charges section to see what each
atom charge is. Note that Amber uses internal charge units, not multiples
of e, in the prmtop though.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Sep 20 2011 - 01:00:02 PDT
