Manish,
If you can reproduce the examples in Amber 10, then please be more
specific on what input script you used and what output files you got in
your failure ... it is impossible to guess what happened based on your
description ...
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
Manish Kumar wrote:
> Thankyou very much for the reply.
>
> I have used bugfix.all before compilation of Amber10. And compiled version
> have passed all the tests of $AMBERHOME/test. Is there any different patch
> for MM-PBSA.
>
> On Sun, Jul 19, 2009 at 6:45 PM, Ray Luo <ray.luo.uci.edu> wrote:
>
>
>> Manish,
>>
>> I was trying to use DElPHI because of two reasons,
>>
>>> First, some papers say that the pbsa module of Amber is not consistence
>>> with the DELPHI results, but it may be true for older version.
>>> Second, I have learned from on the internet that pbsa module can not be
>>> used for charged ligand. I don't know how true it is with Amber10.
>>>
>>>
>>>
>> There were bug fixes for these issues for the earlier versions in amber 9.
>> These fixes have been included in the Amber 10 release. However, if you get
>> a chance to compare pbsa with delphi and found any discrepancy, you're
>> welcome to report back to the list.
>>
>> However, I tried doing mm-pbsa using pbsa module of Amber and I am getting
>>
>>> following error.
>>>
>>> .........................
>>> ........................
>>> Processing PB PBTOT
>>> Doing 1 PB PBSOL
>>> Doing 1 MM GAS
>>> No values for MM_GAS existing -> Skipping
>>> Processing MM GAS
>>> Doing 1 MM ELE
>>> Doing 1 MM VDW
>>> Doing 1 MM INT
>>> Doing 1 MM ELE
>>> Doing 1 MM VDW
>>> Doing 1 MM INT
>>> Doing 1 MM ELE
>>> Doing 1 MM VDW
>>> Doing 1 MM INT
>>> Processing PB PBTOT
>>> Doing 1 PB PBSOL
>>> Doing 1 MM GAS
>>> Doing 1 PB PBSOL
>>> Doing 1 MM GAS
>>> Doing 1 PB PBSOL
>>> Doing 1 MM GAS
>>> =>> Calc delta from raw data
>>> No data for 0+0 MM BOND 0
>>>
>>> I will applicate any help.
>>>
>>>
>>>
>>>
>> First thing first, can you reproduce the mmpbsa examples in amber10? Note
>> that there is an upgrade/bugfix for mmpbsa. Please patch it first and see
>> whether your installation works.
>>
>> All the best,
>> Ray
>>
>> ==========================================
>> Ray Luo, Ph.D.
>> Associate Professor
>> Dept Molecular Biology & Biochemistry
>> University of California, Irvine, CA 92697
>> USPS: PO Box 3900 Email: rluo.uci.edu
>> Phones: (949) 824-9528, 9562
>> Web: http://rayl0.bio.uci.edu/
>> ==========================================
>>
>>
>>
>>
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>>
>>
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Received on Tue Jul 21 2009 - 10:09:30 PDT
