On Sat, Jun 8, 2013 at 12:09 PM, Amparo Garcia Lopez <
Amparo.GarciaLopez.unige.ch> wrote:
> thanks for your suggestions. Setting maxcyc to 10 and ntpr=1 didnt change
> anything. However, when I tried running sander instead of pmemd it worked
> fine (!!), no errors given and everything looks ok..
>
If you have access to AmberTools 13 (completely updated), try using the
"checkValidity" command in ParmEd to ensure that your prmtop is seen as
'valid'. So this command:
parmed.py -p TSL2_1N8R.wat.top << EOF
checkValidity
EOF
And see what is output... There are some rare instances when tleap creates
a broken prmtop file that sander or pmemd may run just fine, but the other
fails. There was also an issue in pmemd with using the GLYCAM06-EP force
field that would have caused an almost immediate segfault that sander would
run just fine.
Not sure if any of these are applicable, but maybe worth checking...
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 10 2013 - 21:30:02 PDT
