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.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.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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *san_amber roy
> *Sent:* Sunday, September 23, 2007 21:18
> *To:* amber.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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Received on Wed Oct 03 2007 - 06:07:15 PDT
