[AMBER] Add residue copied from other unit

From: Vlastimil ZÝma <zima.karlov.mff.cuni.cz>
Date: Tue, 15 Mar 2011 16:24:14 +0100

Hi,

I tried to run following script in tleap, but it failed

> source leaprc.ff99SB
> # Load structures from PDB
> my_model = loadPdb 3mt5_mutant.pdb
> source_structure = loadPdb
/home/jurand/phd/repository/trpa1/structures/3MT5.pdb
> # this does not work for some reason
> calcium = copy source_structure.CA
> add best_model calcium
add: The object calcium is already contained within

I guess it is problem that residue is copied with link to unit, but how can
I copy residue without link to unit. I tried to remove both original and
copied residues from unit, but it does not help

> calcium = copy source_structure.CA
> remove source_structure calcium
remove: Could not find calcium within source_structure.

> calcium = copy source_structure.CA
> remove source_structure source_structure.CA
> add best_model calcium
add: The object calcium is already contained within

I solved this so far by creating new residue from scratch, because it is
only one ion, but it is not very useful way for copying bigger residues.
What is proper way how to do that if I do not have ligand in separate PDB
file? Or how can I separate ligand from PDB file in leap?
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Received on Tue Mar 15 2011 - 08:30:01 PDT
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