Re: [AMBER-Developers] [AMBER] manual prmtop file editing for free energy calculation

From: Ross Walker <>
Date: Mon, 28 May 2012 22:49:46 -0700

Hi Jason,

> Not quite. I mentioned that pmemd.cuda does not support the OPLS, since
> it uses different combining rules than amber. tleap supports the OPLS
> FF with its combining rules, or so I've been told. (and it wasn't my
> responsibility to put that check into pmemd.cuda ;), though I would
> have if I had known about it in time).

I need to look into this some more but are you CERTAIN that the OPLS stuff
is wrong with the CUDA code. I forget who told me this now, maybe Eric
Lindahl, maybe someone else... But... The OPLS combining rules in the
original OPLS paper are NOT the ones that typically get used for OPLS,
including by Jorgensen himself... So it is very possible that by
cancellation of errors the CUDA code is actually doing what Jorgensen et al
actually do when they run OPLS.

I'll see if I can find out for sure who told me this. But there is
definitely inconsistency in the OPLS paper themselves if I remember
correctly. Sad but true. :-(

Out of interest how does Leap know to use different combining rules for
OPLS? - A search of the AMBER 12 manuals for OPLS turns up nothing and all I
can find for OPLS in the tree is the opls_parm.dat file in dat/leap/parm
which specifies AC as the VDW format (as opposed to RE that the FFXX force
fields use)

  H 0.00 0.00
  HO 0.00 0.00

          'RE' van der Waals radius and the potential well depth
                     parameters are read.

          'AC' The 6-12 potential coefficients are read.

But this doesn't seem to change the actual combining rules from what I can
see. So how does leap know to do things differently with OPLS?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Mon May 28 2012 - 23:00:02 PDT
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