Hi,
Thank you both for the answers.
>> Before to do that you could try with the new MM_PBSA.py. I don't know how it
>> works with Zinc, maybe it is more "user friendly" than the old MM_PBSA perl
>>
>
> It takes the Zinc radius from the prmtop file. It does this because
> there is no option to use molsurf, which would require an external
> definition of the radius. However, results with/without molsurf
> differ only very slightly in my experience. I believe mm_pbsa.pl also
> has an option to do this, though I'm not familiar enough with using
> that version to speak definitively on it.
>
>
I've tried the MM_PBSA.py and it seems to recognize both Fe and Zn and
that's good, however I stumbled onto another problem. I set the
MM_PBSA.py running and shortly after checking the complex. receptor and
ligand file I get the error:
> Assuming /usr/local/amber9/exe/sander is part of
> amber9 or amber10. Using old PB input file.
> Warning: igb=5 should be used with either mbondi2 or bondi pbradii
> set. Yours are modified Bondi radii (mbondi)
> Residue labels:
>
> Checking coordinates: ../JMJC-noalyprod-1.mdcrd
> Residue labels:
>
> Checking coordinates: _MMPBSA_complex.mdcrd
> Residue labels:
>
> Checking coordinates: _MMPBSA_complex.mdcrd
> Residue labels:
>
> Checking coordinates: _MMPBSA_complex.mdcrd
> Residue labels:
>
> Checking coordinates: _MMPBSA_receptor.mdcrd
> Residue labels:
>
> Checking coordinates: _MMPBSA_ligand.mdcrd
> Error: Sander error! PB mdout file was not created.
> ~
I've tried all the versions to run MM_PBSA.py in serial and parallel.
I've checked all the input parameters. Still I have no idea of what is
happening. There is not extra information except the error: "Sander
error! PB mdout file not created"
Any ideas as to what can be going so wrong here?
Cristina
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Received on Mon Mar 01 2010 - 08:30:02 PST
