Thank you.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sat, May 21, 2011 4:08:43 PM
Subject: Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. .
yes, but it should work ;)
On Sat, May 21, 2011 at 4:02 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> 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
> > >>>
> > >>>
> > >>> _______________________________________________
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> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>_______________________________________________
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> > >>
> > >
> > >
> > >
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> > >
> >
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> >
>
>
>
> --
> 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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat May 21 2011 - 14:00:03 PDT
