On Mon, Dec 1, 2014 at 3:06 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Dan,
>
> I’m running AmberTools 13. I’ve prepared numerous parameter files in the
> last few days without problem.
>
> In fact, I’ve run a 100ns MD simulation and what I’m trying to do is to
> generate new parameter files keeping a conserved water molecule in the
> topology of the receptor. The reason for this is to run MMPBSA making sure
> that the water molecule is not stripped.
>
That won't work. Your options are:
1. Adjust "strip_mask" to make sure that one of the water residues is not
stripped. This will *only* work if the water molecule never exchanges
(i.e., that the same water molecule is bound in the conserved spot every
frame).
2. Prepare your coordinate and topology files in cpptraj using the
"closest" command to make sure you always get the "closest" water molecule
to your conserved water site, and use those directly in MMPBSA.py without
specifying a solvated topology file.
That said, if you send the necessary input files for tleap (i.e., leap
script, PDB, and any mol2 and frcmod files you used), I'll look into the
segfault.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 01 2014 - 12:30:03 PST
