Dear Jason,
Thank you for your replay. Then if I do not calculate entropy then it is ok with this temperature difference.
Another problem is, my calculation stop when doing mm_pbsa for the ligand (because of the traj of this snapshot), is it possible for me to restart the calculation? As you know calculation for complex and receptor is really time consuming.
A third problem I am facing now is the result form mm_pbsa.pl and mmpbsa_py difference a lot some part of my snapshots ( -44.23 vs. -67.1321). Attach is my input and output for both of them. Do you have any ideas why this happens?
If further information is needed please e-mail me.
Thanks again for you kind help
Xueqin
======= 2010-08-11 23:03:06 您在来信中写道：=======
>Hello,
>
>I believe that the only part of the calculation that really uses the
>temperature are the entropy calculations. You can see that the temperature
>is defined in mm_pbsa_statistics.pm, and you can change it there (look for
>TEMP). However, take care if you're looking to change the temperature for
>entropy calculations, as the temperature 298.15 is hard-coded into the
>source codes of both nmode and nab. Therefore, changing the temperature
>requires you to change the default value in every location that uses the
>temperature and then recompiling the corresponding programs that you
>changed, then re-running the mm_pbsa simulations. There may be pieces here
>that I'm missing, but I think I got the important ones.
>
>Hope this helps,
>Jason
>
>2010/8/10 pxq <pangxueqintea.yahoo.com.cn>
>
>> Hello everyone,
>>
>> I am using mm_pbsa.pl to calculate the binding free energy between
>> the ligand and protein. But the given temperature of mm_pbsa.pl is 300K
>> while my simulation temperature is 310K, is it ok to use 300K to calculate?
>> If not, how to change temperature in the input script? Cause there is no
>> such option so far as I know.
>>
>> Thanks ahead for your kind help
>>
>> Xueqin
>>
>>
>>
>>
>> =============================================================================================================
>> Pang Xueqin
>> State Key Laboratory of Molecular Reaction Dynamics
>> Dalian Institute of Chemical Physics
>> Chinese Academy of Sciences.
>> Tel: 0411-84379352
>> Mobile: 15840973721
>> Fax: 0411-84675584
>> E-mail: pxq.dicp.ac.cn
>> http://english.dicp.cas.cn/
>>
>> =============================================================================================================
>>
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>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Graduate Student
>352-392-4032
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致
礼！
pxq
pangxueqintea.yahoo.com.cn
2010-08-12
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Received on Thu Aug 12 2010 - 08:00:03 PDT
