Vaibhav,
It seems to suggest that there's something wrong with the inpcrd, or at
least with how you made it. A lot of the earlier messages on the mailing
list seem to indicate how the issue is sourced back to things not present
in the inpcrd, specifically the periodic box dimensions (
http://archive.ambermd.org/201206/0058.html).
Another possibility- how large is your system? I think I've run into the
same message before with trying to minimize extremely large systems
without enough memory available on the machine, so you could try testing it
on a machine with more available memory, or trying to cut the atom count in
your system.
Best,
Kenneth
On Tue, Apr 21, 2015 at 5:29 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Hi All,
> while trying to run the minimization job on prmtop and inpcrd file
> generated using ff14SB force field I am getting the this error message in
> the out file and sander quits quickly.
> I have checked the unit before generating prmtop and inpcrd file and it
> gave no error.
> I am giving the following input to the sander.
>
> Another thread discussing similar error did not offer a clear solution in
> my case. http://archive.ambermd.org/201411/0298.html
>
> Any hints to trouble shoot this are much appreciated.
> Thanks a lot.
>
> min.in
> --------
> P450 1W0E apo: initial minimization prior to
> MD
> &cntrl
>
>
> imin=1,maxcyc=1000,ncyc=500,
>
>
> ntpr=5,
>
>
> cut=8.0,
>
>
> ntc=2,
>
> ntr=1, restraintmask =
> '.CA,C,O,N',
>
> restraint_wt=1.0
>
> /
>
>
>
>
> --
> With Regards.
>
> Dr. Vaibhav A. Dixit,
> Postdoctoral Research Scientist,
> Etherow F40/6,
> AstraZeneca,
> Charter Way,
> Silk Road Business Park,
> Macclesfield,
> Cheshire,
> England,
> SK10 2NX
> Ext. No. 20278
> Email: Vaibhav.Dixit.astrazeneca.com
> Moblie Number: +44-7448233157, +91-7709129400.
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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Received on Tue Apr 21 2015 - 06:00:02 PDT
