We have gotten this question 4 times on the mailing list in the past 4
hours, and I responded to it once already.
Please make sure that emails to the Amber mailing list are not being
filtered from your inbox into spam (and please make sure you allow
sufficient time for us to answer your questions -- it may take a day or
two).
The reason alanine scanning is not working for your system is because
you used a united-atom force field and the mutation capabilities in
MMPBSA.py are coded specifically for all-atom force fields. This is
unlikely to change.
Good luck,
Jason
On Wed, 2014-03-12 at 19:49 +0800, lnubbs2014 wrote:
> when performming an alanine scanning calculation on the binding free energy , I got a error.
> error message:
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /home/mmpbsa_py_energy
> cpptraj found! Using /home/cpptraj
> Preparing trajectories for simulation...
> Error during FileIO_Std::Read: Input/output error
> Error during FileIO_Std::Read: Input/output error
> Mutating trajectories...
> MutateError: Mismatch in atom # in residue VAL. (16 in alamdcrd.py and 27 passed in)
> Exiting. All files have been retained.
> commands that I used to create mutant promtop files:
> (tleap)
> source leaprc.ff03ua
> com_mut = loadpdb complex_mutant_val115.pdb
> re_mut = loadpdb receptor_mutant_val115.pdb
> saveamberparm com_mut complex_mutant_val115.prmtop complex_mutant_val115.inpcrd
> saveamberparm re_mut receptor_val115.prmtop receptor_val115.inpcrd
> quit
>
> MD file: https://drive.google.com/folderview?id=0B6PKsnnnVbH1M0tiQmV1Ymk1bU0&usp=sharing
>
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 12 2014 - 08:00:02 PDT
