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 - 14:30:02 PDT
