AMBER Archive (2004)

Subject: Re: AMBER: parameter error for a ligand

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 05 2004 - 15:23:01 CDT

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.gaff
and 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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