Hi,
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.
Arturas
-----Original Message-----
From: owner-amber.scripps.edu on behalf of FyD
Sent: Mon 11/17/2008 1:40 AM
To: amber.scripps.edu
Subject: Re: AMBER: problem
Arturas,
> How to create many copies of the same identical non-standard residue ?
You mean using LEaP ?
> I want to solvate those and put into simulation. Right now I have
> stuck on that, as I have prepared OFF file from single residue.
> However when I load OFF file and load pdb file with many copies of
> the same residue I get variable with no name. I did not find the way
> to modifay/assigne the name to it. I have created new unit
> (createUnit) and try to copy individual residues into it ( add B A.1
> ) , but it did not work.
New-variable = copy Old-variable
set New-variable name "New-name"
set New-variable.1 name "New-name"
See for instance:
http://q4md-forcefieldtools.org/REDDB/up/W-46/script1.ff
Is it what you look for ?
regards, Francois
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Received on Fri Dec 05 2008 - 15:49:09 PST
