Do you know duing which part of the calculation did the error occur (i.e.
did it terminate during the PB part or the nmode part). My guess is that it
died during the nmode calculation. Because often with these calculations an
allocation error is related to insufficient memory for the normal mode
analysis. I would suggest trying to run the calculation on a machine with
more memory. Also, if you are running in parallel, try running in serial
instead to see if that helps.
Good luck!
-Bill
On Fri, Sep 16, 2011 at 4:26 AM, hongphuc nguyen
<phucnguyen20072.gmail.com>wrote:
> Dear All,
> I am running mmpbsa to calculate free binding energy of my system ( 26349
> atoms cover with water box). After running I get the following errors.
> Warning: RADIUS_SET cannot be found in your prmtop files!
> FATAL: allocation failure in vector()
> Error: error during mmpbsa_py_nabnmode calculations!
> This is my mmpbsa.in file, calculation was preformed with 100 frames from
> a
> 500-frame production file
> mmpbsa
> &general
> startframe=400, endframe=500, verbose=1,
> /
> &pb
> istrng=0.100,
> /
> &nmode
> nmstartframe=5, nmendframe=20, nminterval=2,
> maxcyc=50000, drms=0.4,
> /
> I have never met such a problem before. What should I do now to fix it?
> Please give me some suggestions
> Thank you very much
> Phuc
>
> --
> Thank you very much
> I am looking forward to hearing from you
> Best wishes,
>
> Nguyen Ngoc Hong Phuc
>
> Email: phucnguyen20072.gmail.com
> Mobile phone: +84 984620799
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Sep 16 2011 - 04:00:04 PDT
