Re: [AMBER] Cofactor parametrization

From: Francesca Tessaro <Francesca.Tessaro.unige.ch>
Date: Mon, 2 Mar 2015 11:08:08 +0000

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: giovedý 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Mon Mar 02 2015 - 03:30:02 PST
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