Ahh, I hadn't used this ParmEd before, nice piece of artwork it shows when it starts!
this is what I get.
Reading input from STDIN...
> Determining validity of prmtop
2 total warnings
FixableParmWarning: %FLAG SCEE_SCALE_FACTOR not found, but it is not required.
It can be added to the prmtop using the [[ scee 1.2 ]]
action in ParmEd
FixableParmWarning: %FLAG SCNB_SCALE_FACTOR not found, but it is not required.
It can be added to the prmtop using the [[ scnb 2.0 ]]
action in ParmEd
As I undertstand it, with amber11 I didnt have to specify scee 1.2 or scnb 2.0, as this was the default. So I guess this means that my prmtop is correct...
In any case, we have now also installed amber12 with ambertools13, and minimization with my files runs well in pmemd here.
it's very strange, though, that with our new installation of amber11 + ambertools1.5, pmemd could generate MD trajectories no problem, but it could not run any minimizations at all.
We'll try to re-install amber11 from scratch again, and hope this problem doesn't come back.
Thanks very much again for your help :-)
Amparo
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 11 June 2013 06:00
To: AMBER Mailing List
Subject: Re: [AMBER] unable to run minimizations after new installation of amber11
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 Tue Jun 11 2013 - 06:00:04 PDT
