dear david,
will there be a significant difference in binding free energy results on using ligand.mol2 instead of sqm.pdb if the original pose of the ligand was generated as a result of docking.
Thanks and regards,
Nitin Sharma
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Friday, February 14, 2014 9:43 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Amntechamber MOPAC and SQM
On Fri, Feb 14, 2014, Nitin Sharma wrote:
>
> Now my query is when is sqm invoked as a result of antechamber by
> using the command "antechamber -i ligand.pdb -fi pdb -o ligand.mol2
> -fo mol2 -c bcc -s 2 -nc 0" what is true purpose? Is it just to derive
> AM1-bcc charges or it does geometry optimisation too?
>
> Also after this command we get ligand.mol2 file and also sqm.pdb file.
> Which file should be used for further process like merging with
> protein to protein-receptor complex etc? if sqm.pdb is the right
> choice for file to be used then I have to convert it into .mol2 format
> again as parmchk don't read .pdb files as input files.
To add to the previous reply: sqm does a minimization, since that is what was done when the AM1-BCC model was developed and parameterized. The minimized coordinates are in sqm.pdb. Most people want to use the geometry they began with (if it came from an xray model, for example); but you can use the coordinates from sqm if you wish.
[To developers: if we wrote out an sqm.mol2 file that would probably be helpful in some cases. I think this might be a really simple patch...just call an extra subroutine.]
>
> As the default option for bcc charge calculation is sqm then how come
> sometimes I find mopac.
We can't answer this question without more information. One possibility (wild
guess) is that you have very old versions of antechamber around. Mopac was the default a long time ago.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 14 2014 - 18:30:02 PST
