AMBER Archive (2009)

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

From: Manish Kumar (kumarmanish.amb_at_gmail.com)
Date: Thu Jul 23 2009 - 02:10:51 CDT

Dear Prof. Luo,
 I actually ran the tests only, but while doing the Examples in
amber10/src/mm_pbsa/Examples I am getting same error. Following is the
output I am getting. I have used all the bugfix before compiling Amber10.

I will be very thankful for your kind guidance.

Sincerely,
Manish

------
=>> Doing statistics
=>> Reading input
=>> Reordering files
    Final order:
    1. ras_raf_II_wt_com.all.out: -
    2. ras_raf_II_wt_rec.all.out: -
    3. ras_raf_II_wt_lig.all.out: -
=>> Reading files
    Reading ras_raf_II_wt_com.all.out
    WARNING: Missing BOND for MM in 0 -> Taken from -1
    WARNING: Missing ELE14 for MM in 0 -> Taken from -1
    WARNING: Missing ELENB for MM in 0 -> Taken from -1
    WARNING: Missing VDWNB for MM in 0 -> Taken from -1
    WARNING: Missing DIHED for MM in 0 -> Taken from -1
    WARNING: Missing ANGLE for MM in 0 -> Taken from -1
    WARNING: Missing VDW14 for MM in 0 -> Taken from -1
    WARNING: Missing GB for GB in 0 -> Taken from -1
    WARNING: Missing PB for PB in 0 -> Taken from -1
    WARNING: Missing PBCAV for PB in 0 -> Taken from -1
    WARNING: Missing PBDIS for PB in 0 -> Taken from -1
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    Reading ras_raf_II_wt_rec.all.out
    Checking consistency of CALC
    Checking consistency of DATA
    Reading ras_raf_II_wt_lig.all.out
    Checking consistency of CALC
    Checking consistency of DATA
=>> Values of parameters
    TEMP = 300
    R = 8.314
    gammaP = 0.00542
    betaP = 0.92
    gammaG = 0.0072
    betaG = 0.00
=>> Treat special parameters
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1418.
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1391.
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
=>> Calc missing parameters
    Processing MM GAS
        Doing 1 MM ELE
    No values for MM_ELE existing -> Skipping
    Processing MM INT
        Doing 1 MM BOND
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM ANGLE
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM DIHED
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
    Processing MM ELE
        Doing 1 MM ELENB
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM ELE14
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM ELENB
        Doing 1 MM ELE14
        Doing 1 MM ELENB
        Doing 1 MM ELE14
    Processing MM VDW
        Doing 1 MM VDWNB
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM VDW14
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
    Processing GB GBTOT
        Doing 1 GB GBSOL
    No values for GB_GBSOL existing -> Skipping
    Processing GB GBELE
        Doing 1 GB GB
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 MM ELE
        Doing 1 GB GB
        Doing 1 MM ELE
        Doing 1 GB GB
        Doing 1 MM ELE
    Processing GB GBSOL
        Doing 1 GB GB
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 GB GBSUR
        Doing 1 GB GB
        Doing 1 GB GBSUR
        Doing 1 GB GB
        Doing 1 GB GBSUR
    Processing PB PBSOL
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBDIS
Use of uninitialized value in multiplication (*) at
/projsmall/dominy/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBDIS
        Doing 1 PB PBCAL
        Doing 1 PB PBSUR
        Doing 1 PB PBDIS
    Processing PB PBELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
        Doing 1 PB PBCAL
        Doing 1 MM ELE
    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 GB GBTOT
        Doing 1 GB GBSOL
        Doing 1 MM GAS
        Doing 1 GB GBSOL
        Doing 1 MM GAS
        Doing 1 GB GBSOL
        Doing 1 MM GAS
    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

On Tue, Jul 21, 2009 at 10:24 AM, Ray Luo <ray.luo_at_uci.edu> wrote:

> 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_at_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_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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>>>
>>>
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