AMBER Archive (2008)

Subject: Re: AMBER: problem

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Tue Nov 18 2008 - 09:07:19 CST

Hi,

Thanks for replies. I resolved this issue by reinstalling Amber tools
(it seem libraries were not loading correctly).

Arturas

David A. Case wrote:
> 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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