AMBER Archive (2009)

Subject: Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz

From: Manish Kumar (kumarmanish.amb_at_gmail.com)
Date: Mon Jul 20 2009 - 16:11:20 CDT

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_at_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_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
>
>
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