AMBER Archive (2008)

Subject: Re: AMBER: mmpbsa

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Tue Sep 02 2008 - 07:49:33 CDT

Hi Henrik,

Well, it happens when your coordinates extracted dont match the coordinates
which you specify in the mm_pbsa.pl script when you calculate the energies.
You will be surprise that the generation of snapshots dont give error. When
you submit your receptor, ligand and complex file if you have used ptraj, it
ll add up residue one atom number more for every TER whereas your snapshots
wont have atom number assigned to TER.

The other problem could be you are running out of virtual memory. If you are
able to run the tutorial properly then there is no memory problem.

Regards,
Neha

2008/9/2 Henrik Öberg <henrikob_at_kth.se>

> Hi AMBER users,
> I have a problem calculating the binding free energy of my complex. After
> generating the snapshots using mmpbsa.pl, which I think works just fine, the
> problem presents itself when I start the binding energy calculations.
> Directly after executing the folllowing command:
> $AMBERHOME/exe/mm_pbsa.pl binding_energy_13.mmpbsa > binding_energy_13.log,
> where binding_energy_13.mmpbsa holds the input specifications, I get an
> error message just telling me the run was not successfull, which is not very
> informative..
> Has anyone encountered a similar problem?
> Thankful for any help!
> Cheers
> Henrik Oberg,
> KTH Sweden
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu