Dear Amber users,
I have been trying to calculate the per residue free energy decomposition
of a protein-protein complex. The receptor protein is a metallaoenzyme in
which two zinc clusters were modeled using MCPB as described in the MTK++
documentation (HHHO and HHHD configurations). As far as I use only the PB
namelist the calculation run appropriately. However when adding the GB
section the following error message appears:
Beginning GB calculations with /amber12/bin/sander
calculating complex contribution...
bad atom type: OA
CalcError: /amber12/bin/sander failed with prmtop
/home/free_energy_calculation/complex_vacum.prmtop!
Exiting. All files have been retained.
Free energy estimation however were achieved successfully with either &PB
or &GB namelists.
Noting that i have amber12 compiled with AmerTools13 just three days ago (I
also tried it with AmbrtTools12 and it resulted to the same error).
>From previous mail threads, it seems that only this one is relevant
http://archive.ambermd.org/201408/0262.html
However, I can not follow the same solution as it proposes to upgrade to
amber14 which is not available for me right now.
Can somebody help me to fix this problem in amber12 ?
best regards
Houcem
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Received on Tue Jan 20 2015 - 03:00:02 PST
