AMBER Archive (2004)

Subject: Re: AMBER: parameter error for a ligand

From: Sivanesan Dakshanamurthy (sd233_at_georgetown.edu)
Date: Tue Oct 05 2004 - 16:45:51 CDT

Dear Dr. David A. Case:
I put the loadpdb & save amberparm for protein in the leaprc file.

thanks
siva

D.Sivanesan, Ph.D.
Dept. of Oncology,
Lombardi Cancer Center (NCI Comprehensive Cancer Center),
Georgetown University, DC 20057
Phone: 202-687-6338

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Tuesday, October 5, 2004 4:23 pm
Subject: Re: AMBER: parameter error for a ligand

> On Tue, Oct 05, 2004, Sivanesan Dakshanamurthy wrote:
> >
> > I am simulating a protein that contains a ligand. I have
> generated parameter
> > for the ligand using 'antechamber'. Then I ran tleap for the complex
> > (contain both protein & ligand).
> >
> > source leaprc.gaff
> > mods = loadamberparams frcmod
> > loadamberprep LIG.prepin
> > saveamberparm HTW prmtop prmcrd
>
> If you have both a protein and a ligand, you need to source both
> leaprc.gaffand leaprc.ffxx, in order to get parameters for
> everything. It's not clear
> from the above where HTW came from, however. If it is in
> LIG.prepin, where
> is the protein?
>
> >
> > FATAL: Atom .R<HTW 553>.A<C10 1> does not have a type.
> > FATAL: Atom .R<HTW 553>.A<C9 2> does not have a type.
> > FATAL: Atom .R<HTW 553>.A<C8 3> does not have a type.
>
> You can use the desc command, or the edit commands in xleap, to
> examine the
> types of atoms. Maybe that will provide some insights.
>
> ...good luck..dac
>
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