Re: [AMBER] How to deal with Heme?

From: Anna Cebrian Prats <>
Date: Wed, 18 May 2016 16:15:14 +0000

Thank you Dac,

Your answer was very useful.

I already got it.


De: David A Case <>
Enviat el: dimecres, 18 de maig de 2016 18:06:11
Per a: AMBER Mailing List
Tema: Re: [AMBER] How to deal with Heme?

On Wed, May 18, 2016, Anna Cebrian Prats wrote:
> I want to use the HEM.mol2 file of (compound I hexa-coordinate) to use
> the charges but the Cartesian coordinate not coincide then I have to
> create a new .mol2 file with my coordinate and take the charges from the
> Shahrok file, haven't I? Who can obtain a .mol2 file?

No, you (probably) don't need to do this. Consider the usual LEaP workflow:

loadMol2 HEM.mol2
cyp = loadPdb protein.pdb

LEaP uses the coordinates in the pdb file, and ignores the coordinates in
the mol2 file. (There are some subtleties when some of the atoms in the HEM
group are missing from the pdb file, but, generally speaking, you don't need
to create a mol2 file with *your* coordinates in it).

> > loadmol2 HEM.mol2

After you do this, use the "list" command to make sure you have a HEM residue,
and use the "desc" command to see what atoms it contains:

desc HEM.1

Make sure the residue and atom names that are no loaded into LEaP match those
in your input pdb file. You may well have to use a text editor on the PDB
file to get things to match up.


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