Re: [AMBER] Ligands and cofactors in enzymes

From: David A Case <>
Date: Tue, 19 Jul 2011 11:40:09 -0400

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.


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Received on Tue Jul 19 2011 - 09:00:04 PDT
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