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.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.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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
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Received on Thu Jul 23 2009 - 01:09:37 PDT
