Re: [AMBER] Antechamber

From: Jasim, Mahmood (Student) <"Jasim,>
Date: Fri, 13 Sep 2013 14:50:42 +0000

Thank you so much for your reply. I do run the procedure as you said and load the ligand files into leap followd by the complex. I finally solvate the model and save the prmtop and inpcrd files. I convert the inpcrd file into a pdb file to view it and here I find that the ligand position within the protein has changed from the starting conformation.

Can I also ask about the -ek falg, where does it go within the command and how I specify PM3?

Mahmood Jasim
From: David A Case []
Sent: 13 September 2013 15:30
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber

On Fri, Sep 13, 2013, Jasim, Mahmood (Student) wrote:
> I am currently using Antechamber for preparing files to run MD on a
> docked complex. It works fine and I get the prepi and frcmod files. The
> problem is that the conformation of the ligand within the protein
> is being changed. What could be the problem?

You don't say enough about what you did to be of much help. But note: the
usual procdure is to make prepi and frcmod files using antechamber, load these
into tleap, then to use the loadPdb command to load the *original* docked
coordinates (with both protein and ligand). This way the coordinates are the
ones you originally had.

> Also I understand that
> Antechamber runs using AM1, what would be the command for using PM3
> instead?

You could use the "-ek" flag in antechamber, or just edit the file.
(Please note that this is *not* a good thing to do if you want to generate
AM1-bcc charges.)


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