Re: [AMBER] decomposition problems

From: fancy2012 <fancy2012.yeah.net>
Date: Sat, 13 Nov 2010 17:34:44 +0800 (CST)

Hi Bill,
Thanks very much for your reply! I have tried the example, but still I can not get the nonpolar solvation energies. It is strange. I will try to figure it out, and could you give me some other suggestions? Thanks in advance!
 
Best wishes,
fancy


At 2010-11-12úČ"Bill Miller III" <brmilleriii.gmail.com> wrote:
Have you tried the decomposition example in $AMBERHOME/src/mm_pbsa/Examples/ ? Try this and see if you are able to get any nonpolar solvation energies using the provided scripts/files. If you can get nonpolar solvation energies using the examples, then compare the two input files for differences.

Good luck!

-Bill


2010/11/12 fancy2012<fancy2012.yeah.net>

Hi Bill,
Thanks very much for your reply! All the bugfixes had been applied when AMBER10 was installed. And I used the perl version of mm/pbsa to calculate. During the process of calculations of decomposition, there were not any errors and warnings.And I have attached the input file used to extract the snapshots and the input and outputs of decompositions! By the way, the output file "HER2-Lapa_statistics.out" was edited that only the delta values were reserved. Thanks very much!
 
Best wishes,
fancy




At 2010-11-12úČ"Bill Miller III" <brmilleriii.gmail.com> wrote:

>This is somewhat difficult to diagnose without more information. Are you
>using the perl or python script? Have you applied all bugfixes? What does
>your input file look like? Were there any errors or warnings in any of the
>output files? The more information you provide about your calculation the
>easier it will be for us to help pinpoint your exact problem.
>
>-Bill
>
>On Thu, Nov 11, 2010 at 9:13 PM, fancy2012 <fancy2012.yeah.net> wrote:
>
>> Dear AMBER users,
>> I did some decompositions using MM/PBSA, but all the nonpolar solvation
>> energy is zero. It is strange, but somebody tell me that is normal, but I
>> found that there were values of nonpolar solvation energy which were not
>> zero. I am confused, if I have make some mistakes, what possible mistakes
>> they were? Could someone help me figure it out? Thanks very much!
>>
>> Best wishes,
>> fancy
>>
>>
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>
>
>
>--
>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



--
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
Received on Sat Nov 13 2010 - 02:00:03 PST
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