[AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda?

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Fri, 8 Aug 2014 12:12:44 +0100

Dear amber-ites (and particularly the pmemd.cuda developers),

I have generated a prmtop with chamber. Subsequently, I modified the prmtop
with parmed.py to change the LJ parameters in accordance to the NBFIX
corrections (for sodium - carboxylate interactions) that are now
recommended for the CHARMM protein force-field (v36).

sander & pmemd have no problem running with this modified prmtop, but
pmemd.cuda gives the following error:

CUDA (GPU): Prmtop appears to contain modified off-diagonal elements for
VDW A coef.
            GPU code does NOT support such force field modifications.
            Found Aij = 61596.8299420842 expected
            i = 36 j = 3 Matrix element = 633

(I've confirmed that pmemd.cuda runs fine with the prmtop prior to the
NBFIX correction.)
This is NOT the most recent pmemd.cuda version (I don't have access to that
yet), I used
Version 12.3.1

Can I confirm that it is thus not possible not to use the NBFIX corrections
in combination with pmemd.cuda?
And, are there any plans to support this in the future? (Or is it already
supported in a more recent pmemd.cuda version?)

Many thanks,
AMBER mailing list
Received on Fri Aug 08 2014 - 04:30:02 PDT
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