Hi,
It appears that mm_pbsa.pl is failing when it is attempting to calculate the
SASA. Molsurf for whatever reason is unable to detect a radius for the H5
atom of residue SAM. The other users might be able to give you a more
detailed reason as why it is unable to do so. I would suggest as a *quick
fix* that you turn off molsurf and calculate the SASA with the LCPO method
available in sander. set MS=0 and GBSA=1 in the GB section. Hope that helps
and good luck..
On Mon, Mar 8, 2010 at 9:30 AM, Aurum Bai <javacfish.yahoo.com.cn> wrote:
> Hello, everyone!
>
> When run "$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa", I found this
> err as below:
> #################################################################
> =>> Calculating energy / entropy contributions
> Calc contrib for ./snapshot_com.crd.1
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> Generate PQR
> No radius found for 'H5* 3835 in residue SAM 251
> Died at /home/john/soft/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line
> 660, <PDB> line 3837.
> ########################################################################
>
> But I have run much time, I do not want to run again.
>
> Could somebody tell me how to retrieve this errs?
>
> Thanks very much!
>
> javacfish
>
>
>
>
>
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Mon Mar 08 2010 - 10:30:04 PST
