Dear Amber Users,
I have tried to run MM-GBSA calculations on CYP450 protein containing HEME
using Python script (MMPBSA.py).
I come-up with error message;
-----------------------------------------------------
Beginning GB calculations with sander...
calculating complex contribution...
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
------------------------------------------------------------------------------------------------------
I am using Amber Tools1.5 with Amber11.
I have tried to solve the error as mentioned in previous archives.
http://archive.ambermd.org/201003/0002.html
http://archive.ambermd.org/201201/0129.html
http://archive.ambermd.org/201201/0131.html
I have made necessary changes in files "*$AMBERHOME/src/sander/mdread.f"* and
"*mm_pbsa_calceneent.pm" *(added ionic radii for FE atom)*.*
Then I re-compiled Amber11 completely.
But still I am facing same problem of Bad atom type FE.
If anybody solved this problem for CYP450 system then please suggest me
what to do?
--
*Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228*
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Received on Tue Jan 08 2013 - 06:30:04 PST
