Hi,
I am trying to set up free-energy perturbation calculations using the ff02 force field for 10 protein-ligand systems. In order to do so I am using the RESP method.
http://www.teokem.lu.se/~ulf/Methods/resp.html
More specifically, I am following the explicit guidelines: “How to determine RESP charges for the polarisable Amber ff02 force field.” from the above link. The procedure does not have complete documentation, why I would like to request any available documentation from 2002 or later if possible since someone must have performed FEP calculations with the ff02 force field previously.
My QM calculations for the ligands are finished for a first protein and I am using Amber modules to perform the RESP method.
I have access to a compiled version of Amber 14 on the cluster I am using, why it would be preferable to use that if possible, but I do not know the details of how to amend the sander.in namelist input.
Is there a dependency on AMOEBA for Amber 14? I am receiving the error message AMOEBA_get_ucell_info: UNIT_CELL_PARAMETERS missing
in my sander.out file . The error was previously posted in Amber mailing list archive: http://archive.ambermd.org/200806/0296.html
The input to tleap is:
source leaprc.ff02
source leaprc.gaff
loadAmberParams cox2.dat
loadAmberPrep l10-resp.in
x = loadpdb NEWPDB.PDB
check x
saveamberparmpol x l10-inpprm l10-inpcrd
quit
Furthermore, I am unsure about which formats, old or new, for the procedure that should work with Amber 14.
Could you please provide me with an updated procedure?
Med vänliga hälsningar / Best regards,
Martin
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Martin Olsson
PhD student, Theoretical Chemistry
MSc, Engineering Nanoscience
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Received on Mon Feb 23 2015 - 08:00:04 PST
