AMBER Archive (2008)

Subject: Re: AMBER: problem

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 17 2008 - 01:40:33 CST

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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