AMBER Archive (2004)

Subject: RE: AMBER: sander of AMBER 8 doesn't work

From: Feng, Hanqiao (NIH/NCI) (fengh_at_mail.nih.gov)
Date: Wed Jun 02 2004 - 07:45:01 CDT

Dear Ross:
  Thank you very much for your response to my question. Actually, I am using
NIH Biowulf cluster where AMBER 8 was installed. From .out file, I got the
error message as:
     * NB pairs 2781 13482275 exceeds capacity(13482333 ) 0
     size of nonbond list = 13482333
    Sander bomb in subroutine nonbond_list
    Non bond list overflow
    Check MAXPR in locmem.f
Since I have no permission to do the test or any change on the
superdirectory.
Could you please tell what I can do.

Best regards,

Hanqiao
 

> ----------
> From: Ross Walker
> Reply To: amber_at_scripps.edu
> Sent: Tuesday, June 1, 2004 2:56 PM
> To: amber_at_scripps.edu
> Subject: RE: AMBER: sander of AMBER 8 doesn't work
>
> Dear Hanqiao,
>
> We will need more information in order to be able to help you here. What
> architecture are running on? A single CPU desktop or a cluster?, what
> opperating system, what compilers did you use to compile sander? Also,
> most
> importantly have you run the test cases in $AMBERHOME/test do they all
> pass
> or are there errors?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Feng, Hanqiao (NIH/NCI)
> > Sent: 01 June 2004 11:40
> > To: 'amber_at_scripps.edu'
> > Subject: AMBER: sander of AMBER 8 doesn't work
> >
> > Hi all
> > I am new user of amber 8.0. I met problem to run sander.
> > When I follow the
> > tutorial under amber.scripps.edu, the eleap or xleap part
> > works very well, I
> > can got the sample prepared. when I issue sander, even for simple
> > minimization, it stands there no response, no complain. When
> > I check the
> > .out file. it was empty. Could you please tell me what's wrong.
> >
> > Thanks,
> > Hanqiao
> >
> > Lab of Biochemistry
> > NCI/NIH
> > Bethesda, MD
> >
> >
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>
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