Yes ... The differences in the results if any should be very small if
you use the same input parameters ...
Ray Luo, Ph.D.
On May 21, 2011, at 1:02 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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>>>>>
>>>>
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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 Sat May 21 2011 - 16:30:03 PDT
