AMBER Archive (2007)

Subject: Re: AMBER: MAXPR

From: san_amber roy (sanamber_at_gmail.com)
Date: Tue Oct 02 2007 - 01:58:03 CDT

Dear Ross,
                I have understood what's wrong with the system. I did a very
small mistake that's why I was getting such abnormal result. Anyway thanks
for your help.
Regards
santanu

On 10/1/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Dear Santanu,
>
> With the limited information you have provided it is very difficult to
> help further. What do you mean by conjugate gradient(getting terminated)? -
> do you mean it crashes? Is there an error message?
>
> Can you post your input and output files please so it is clearer what is
> going on and what you mean by "energy is quite high and not consistent"
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *san_amber roy
> *Sent:* Monday, October 01, 2007 01:11
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: MAXPR
>
> Hi Ross,
> As you suggested I increased the value of maxpr in locmem.ffile, then sander was running minimization using steepest discent, but fails
> to run congugate gradient(getting terminated.) Even during steepest discent
> minimization , energy is quite high,and not consistant,i.e there could be
> huge difference in energy between.
>
> Secondly, you might call my system unusual, as it is an F0 ATP synthase
> complex a1c12(pdb id 1c17) and this c12 is replaced by c9(pdb id 1c0v)
> {basically F0 ATPase contains one "a" subunit and 9-12 "c" subunit},
> So basically my system is a1c9 complex.
> So to get the correct interface between a and c, I need to minimize the
> system. And in this situation I am facing such problem.
>
> Can you kindly suggest something regarding this? what should I do to avoid
> this?
>
> Thanks,
> Santanu
>
> On 9/24/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> >
> > Hi Santanu,
> >
> > Please take a look at the following message from the mailing list
> > archive and see if it helps:
> >
> > http://amber.ch.ic.ac.uk/archive/200704/0291.html
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not be read every day, and should not be used for urgent or sensitive
> > issues.
> >
> >
> > ------------------------------
> > *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > Behalf Of *san_amber roy
> > *Sent:* Sunday, September 23, 2007 21:18
> > *To:* amber_at_scripps.edu
> > *Subject:* AMBER: MAXPR
> >
> > Dear amber users,
> > whenever I am running sander (of AMBER 8 ) to
> > mimimize a system with cut = 10, it is showing error like ' SANDER BOMB in
> > subroutine nonbond_list NON BOND list overflow',
> >
> > so firstly, this is the error...
> >
> > * NB pairs 1791 4358815 exceeds capacity ( 4359000) 0
> > SIZE OF NONBOND LIST = 4359000
> > SANDER BOMB in subroutine nonbond_list
> > Non bond list overflow!
> > check MAXPR in locmem.
> >
> >
> > and whenever the cut = 8, the output is saying 'unreasonably small cut
> > off for non periodic run............ input error. '
> >
> > so how to get rid of this error?
> >
> > Kindly look into this matter.
> > Santanu
> >
> >
>

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