On Thu, 2015-02-26 at 14:45 +0000, Francesca Tessaro wrote:
> Hello,
>
> I am running MD of a protein with NADP+ as cofactor.
>
> I have some troubles with the cofactor parametrization:
> antechamber is not recognizing the charge of my mol2 file and as well pdb file.
What error messages are you getting? This description doesn't help us
figure out what your problem is.
> So I decided to dowload the prep and frcmod files from Amber parameter database
> but I don't know how to integrate them with my mol2 or pdb file.
The prep file defines a residue. It replaces the mol2 file, so all you
need is the PDB file. You have to make sure that the residue name
defined in the prep file matches the name assigned to that residue in
the PDB file. You also need to make sure that the names of the atoms
defined in the prep file matches the names of the atoms for that residue
in the PDB file. This is how LEaP knows which atom in the residue
template (prep or mol2 file) maps to which atom in the PDB file.
Then you need to load the prep and frcmod file in tleap when you
parametrize your system.
If you have future questions, please tell us briefly exactly what you
did (don't describe it, give us actual input and actual output). Those
are much easier questions to answer, because we don't have to guess
anything.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 26 2015 - 08:30:03 PST
