>The idea is to make the denominator smaller than its original value of 3.0
>(say 2.5 or 2.0), not to make it 10 million times larger. You want maxpr to
>be a little bigger. But when you get an error like this, it means that there
>is something unusal in your structure (or your choice of cutoff, or
>something).
This may be a dumb question but isnt this what this NMR structure refinement is supposed to do, take my not so good structure from CYANA and get rid of the VDW clashes.
I changed those values from 30,000,000 down to 3 then to 2 then to 1 and it didnt help, so i will give the pmemd a shot. Do you have any advice for trying to refine an NMR structure from CYANA? THanks again.
________________________________
From: case <case.biomaps.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wed, March 17, 2010 2:56:21 PM
Subject: Re: [AMBER] sander bomb and maxpr question
On Wed, Mar 17, 2010, Andrew Olson wrote:
> I have looked over the archives to find a solution to this error
>
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
> So i found that you have to edit this portion of the locmem.f file so i did to this,
>
>
> if( numextra == 0 ) then
> maxpr_float = natom * (cutoffnb + skinnb)**3 / 30000000d0
^^^^^^^^^^^
The idea is to make the denominator smaller than its original value of 3.0
(say 2.5 or 2.0), not to make it 10 million times larger. You want maxpr to
be a little bigger. But when you get an error like this, it means that there
is something unusal in your structure (or your choice of cutoff, or
something). Default values for parameters are carefully chosen, so don't
change them without a reason. And, the actual source of the problem may be
something quite different, with the non-bond overflow as just a symptom.
> else ! need more nonbon storage with extra points
> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.50d0
> end if
Another idea is to use pmemd, which handles memory in a differnt fashion.
..hope this helps...dac
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Received on Wed Mar 17 2010 - 16:00:02 PDT
