Thank you Jason for your kelp,
when I am running antechamber the error message that occurs is:
> Error: cannot run "/usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out" of mul() in charge.c properly,
exit
I am trying to modify the atom type with sybyl (especially for my positive nitrogen in the pyridine ring) and running different command with antechamber, always with a net charge of -3 (-nc -3) but it still not working.
If you have any suggestion would be really appreciated,
I attached also my mol2 file
Thank you,
Francesca
Da: Jason Swails [jason.swails.gmail.com]
Inviato: giovedì 26 febbraio 2015 17.22
A: amber.ambermd.org
Oggetto: Re: [AMBER] Cofactor parametrization
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 Mon Mar 02 2015 - 03:30:02 PST
