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?
Regards
Mahmood Jasim
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
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 sqm.in file.
(Please note that this is *not* a good thing to do if you want to generate
AM1-bcc charges.)
....dac
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Received on Fri Sep 13 2013 - 08:00:04 PDT
