Thanks all. I will try this.
Agnes
On 5/20/11 4:18 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>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.
>> >>>>> _______________________________________________
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>> >>>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>--
>> >>>>Bill Miller III
>> >>>>Quantum Theory Project,
>> >>>>University of Florida
>> >>>>Ph.D. Graduate Student
>> >>>>352-392-6715
>> >>>>_______________________________________________
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>> >>>>http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>
>> >>>
>> >>>
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>> >>>
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>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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Received on Fri May 20 2011 - 15:00:02 PDT
