AMBER Archive (2009)

Subject: Re: [AMBER] database

From: case (
Date: Wed Sep 16 2009 - 10:26:24 CDT

On Wed, Sep 16, 2009, Steve Seibold wrote:

> I have a mol2 file of a ligand which I have used to generate (using
> parmchk) a ligand.frcmod file. So, I have the ligand.mol2 and
> the ligand.frcmod. I changed the atom names of the ligand in my
> protein/ligand complex pdb file so that the names are equivalent to
> those found in the ligand.mol2 file.
> I am now trying to use the file.mol2 as a prepin file so that when
> I load my protein/ligand complex I can generate topology and inpcrd
> files.

Here is the general tleap scheme:

source leaprc.ff99SB (for example)
source leaprc.gaff (to get the parameters needed for the ligand)
loadAmberParams ligand.frcmod (to get the special parameters for your ligand)
RES = loadMol2 ligand.mol2 (where "RES" is the name of the ligand residue)
complex = loadPdb mycomplex.pdb (where this is the pdb file referred to above)
saveAmberParm complex prmtop inpcrd

Basically, the "loadMol2" command does for mol2 files what the "loadAmberPrep"
file does for prepin files.

...hope this helps...dac

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