|
|||||||||||||||||||||||||||||||||
AMBER Archive (2008)Subject: RE: AMBER: problem
From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
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-----
> 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
New-variable = copy Old-variable
set New-variable name "New-name"
See for instance:
Is it what you look for ?
regards, Francois
-----------------------------------------------------------------------
-----------------------------------------------------------------------
| |||||||||||||||||||||||||||||||||
|