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
>>>>
>>>
>>>
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>>
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Received on Fri May 20 2011 - 14:30:03 PDT
