Re: [AMBER] Fwd:

From: Asfa Ali <asfa.iisc.gmail.com>
Date: Thu, 26 Dec 2013 19:07:55 +0530

Hi,

I checked and found that the bond energies are missing in all the
frames in snapshot_lig.all.out and also for snapshot_com.all.out
(while snapshot_rec.all.out has bond energy in all the frames).

So I checked the lig_vac.prmtop, com_vac.prmtop and rec_vac.prmtop and
found that the pdb structures formed by the above were fine (used
ambpdb command).

I have repeated the experiment but it showed the same error.

The error now is as follows :

Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
Use of uninitialized value in multiplication (*) at
/home/phd/09/ochasfa/amber-parallel/amber9//src/mm_pbsa/mm_pbsa_statistics.pm
line 1472.
    No data for 0+0 MM BOND 0

I am not having any clue what to do. I am attaching the .out files

Kindly help


On 12/26/13, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Dec 25, 2013 at 7:01 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
>
>> Hi,
>>
>> I am trying to calculate free energy of a complex by using mm_pbsa.pl.
>> It has generated all the three out files- snapshot_com.all.out,
>> snapshot_lig.all.out and snapshot_res.all.out. However, the
>> snapshot_statistics.out is missing.
>>
>> So I tried to do it manually :
>> #mm_pbsa_statistics.pl 1 0 snapshot_statistics.in snapshot_statistics.out
>>
>> But this shows :
>> Calc delta from raw data
>> No data for 0+0 MM BOND 0
>>
>> I checked with the ambermailing list but couldn't find a suitable ans
>> to solve my problem. Kindly help
>>
>
> You need to provide more information about what you did for us to provide
> useful advice.
>
> That said, I would suggest trying MMPBSA.py, as many of the frequent
> responders to this list are more familiar with that program.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
Asfa Ali
Prof. S. Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,
Bangalore-12





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Received on Thu Dec 26 2013 - 06:00:02 PST
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