Re: [AMBER] Ligands and cofactors in enzymes

From: Gustavo Seabra <>
Date: Tue, 19 Jul 2011 13:19:24 -0300

On Tue, Jul 19, 2011 at 12:40 PM, David A Case <> wrote:
> On Tue, Jul 19, 2011, David Cantu wrote:
>> Yes this is what I meant. In antechamber, sqm will optimize (minimize) the
>> structure and change the conformation. This gives me a mol2 and from that
>> the frcmod file.
>> If I want to use the original pdb coordinates as my starting point, do I
>> load the mol2? How in XLeap do I load original pdb coordinates, but keep
>> mol2 and frcmod parameters?
> What Gusatvo (tried to) say:
>> > You can load those parameters, but use the PDB coordinates for the ligand.
> Use loadmol2 and loadamberparams to get the topology and parameters loaded.
> Then say something like this:
> x = loadPdb  filename.pdb
> where "filename.pdb" has the coordinates of both the ligand and the receptor;
> (or just the ligand if there is no receptor).  Then "saveamberparm x ...."
> will give you coordinates that came from the pdb file.
> ....dac

Yep, thats what I meant. :-)

Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417

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Received on Tue Jul 19 2011 - 09:30:02 PDT
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