Further to my email, here are the errors:
Error occured on rank 3.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/gandhin/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/gandhin/amber17/bin/sander failed with prmtop
../../NTD/HS-9548211675/complex.prmtop!
Error occured on rank 5.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/gandhin/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/gandhin/amber17/bin/sander failed with prmtop
../../NTD/HS-9548211675/complex.prmtop!
Error occured on rank 9.
Exiting. All files have been retained.
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/gandhin/amber17/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/gandhin/amber17/bin/sander failed with prmtop
../../NTD/HS-9548211675/complex.prmtop!
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
Cpptraj Generated trajectory
minimizing coord set # 1
PB bomb in pb_atmlist(): MAXNEI too short
<
http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
Virus-free.
www.avg.com
<
http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
On Fri, 18 Dec 2020 at 07:28, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Hi List,
>
> I tried to run gbsa and pbsa using ambertools18. Gbsa produces output
> without any issues with prmtop files. However, pbsa throws calc error with
> complex.prmtop files. I have changed the default parameter for radiopt to
> 0.
>
> How can I get this running?
> let me know if I should provide further information.
>
> Regards,
> Neha
>
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 17 2020 - 22:00:02 PST
