AMBER Archive (2008)

Subject: Re: AMBER: problem

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 18 2008 - 06:15:57 CST

On Mon, Nov 17, 2008, Arturas Ziemys wrote:
>
> My compound is a ligand of ~ 50 atoms. I have prepared frdmod and prepi
> files with antechamber from MOPAC minimized structure. I understand how to
> prepare, let's say, one ligand in water.
>
> However, I miss a link how can I apply those files creating a system of four
> copies of ligand molecules ? Let's say I have a PDB file of four copies and
> do "loadPDB". Here I lost idea. Because if I have prepared library OFF file
> containing topology, charges, etc, from PREPI and FRCMOD files, and then I
> expect that OFF information would be applicable to all residues as all four
> copies of residues in PDB files have the same residue name. When I load my
> PDB with 4 copies of ligand, I get variable of unit with no name.

We need details: please report exactly what LEaP commands to entered, and what
the result was. Just saying that you "[did] loadPDB" is not enough: we need
to know exactly what you typed, and exactly what the result was.

Also, be sure that your PDB file has a "TER" card between each copy of the
ligand.

...dac

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