Sorry I didn't get it. Does that mean I need to install AmberTools 1.5 to solve
this problem?
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, May 20, 2011 5:18:05 PM
Subject: Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. .
You can download AmberTools 1.5 and build it on your own on your machine.
MMPBSA.py is built by default as part of AmberTools 1.5, and uses only
AmberTools for typical MMPBSA, MMGBSA and MM/3D-RISM calculations (you only
need sander for decomp or QM/MMGBSA calculations).
HTH,
Jason
On Fri, May 20, 2011 at 5:08 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Yes, it's been fixed in version 1.5 ... since it is a feature
> enhancement not a bug fix, so it won't be patched to version 1.4 ...
>
> Ray
>
> On Fri, May 20, 2011 at 2:03 PM, Zheng, Zhong <Zhong.Zheng.stjude.org>
> wrote:
> > You mean AmberTool1.5? What about 1.4? That's what I'm using. Thanks.
> >
> >
> >
> > Agnes
> > On 5/20/11 3:15 PM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
> >
> >>It's been fixed in the latest AmberTools release ... it no longer uses
> >>any pairlist ...
> >>
> >>Ray
> >>
> >>On Fri, May 20, 2011 at 1:06 PM, Zheng, Zhong <Zhong.Zheng.stjude.org>
> >>wrote:
> >>> Actually I'm struggling with the same problem for the last couple of
> >>>days.
> >>> I am doing a MMPBSA calculation on protein-ligand binding. I have a big
> >>> system with more than 700 residues plus counter ions and waters.
> >>> The gb run finished ok. But the pb run never works for me. The error
> >>> message at the end of the _MMPBSA_*.mdout is something like this:
> >>> PB bomb in pb_reslist(): maxnbr too small
> >>>
> >>> I did some search online. One post typically said "The error message
> >>>shows
> >>> that the estimation of maximum pairs for
> >>> residue-based cutoff is too small. A larger cutoff, for example by
> >>>setting
> >>> cutres=12 (default 10) usually works fine." It seems you can go change
> >>>the
> >>> code, recompile and fix this. There posts are relatively old. I'm
> >>> wondering if amber11 has actually fixed these problems already.
> >>> Also I'm working on a cluster and I don't have the authorization to
> >>>touch
> >>> the code as Amber is installed in public directory. So besides
> >>>installing
> >>> the ipbsa, which I can't do either, are there other options?
> >>>
> >>> Many thanks.
> >>>
> >>> Agnes
> >>>
> >>> On 5/20/11 2:41 PM, "Bill Miller III" <brmilleriii.gmail.com> wrote:
> >>>
> >>>>What did your MMPBSA.py input file look like? Also, there should have
> >>>>been
> >>>>some _MMPBSA_*_pb.mdout files created for the complex, receptor, and
> >>>>protein. My guess is there are some helpful information/messages in
> >>>>those
> >>>>files.
> >>>>
> >>>>-Bill
> >>>>
> >>>>On Fri, May 20, 2011 at 3:36 PM, bin wang <wang_p_z.yahoo.com.cn>
> wrote:
> >>>>
> >>>>> Hello Amber users,
> >>>>> When I use mmpbsa.py to calculate binding energy of a protein-protein
> >>>>> interaction, the result.dat file only showed the GB part but not the
> >>>>>PB
> >>>>> part.
> >>>>> The messages are listed as follows:
> >>>>>
> >>>>> ptraj found! Using /opt/amber11/bin/ptraj
> >>>>> sander found! Using /opt/amber11/bin/sander (serial only!)
> >>>>>
> >>>>> Preparing trajectories with ptraj...
> >>>>> 50 frames were read in and processed by ptraj for use in calculation.
> >>>>>
> >>>>> Starting sander calls
> >>>>>
> >>>>> Starting gb calculation...
> >>>>>
> >>>>> Starting pb calculation...
> >>>>>
> >>>>> Error: No potential terms in sander output! Check output files.
> >>>>> NOTE: All files have been retained for debugging purposes. Type
> >>>>>MMPBSA.py
> >>>>> --clean to erase these files.
> >>>>>
> >>>>> When I caculated a protein-DNA interaction, the result showed both PB
> >>>>>and
> >>>>> GB,
> >>>>> but for this one, it only showed GB. I don't know what could
> possibly
> >>>>> cause
> >>>>> this problem. Need your help. Thank you.
> >>>>> _______________________________________________
> >>>>> 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
> >>>>_______________________________________________
> >>>>AMBER mailing list
> >>>>AMBER.ambermd.org
> >>>>http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>> Email Disclaimer: www.stjude.org/emaildisclaimer
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>_______________________________________________
> >>AMBER mailing list
> >>AMBER.ambermd.org
> >>http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 21 2011 - 13:30:02 PDT
