Hey Albert,
with a search engine like
http://bit.ly/10uN8R6 you find hundreds of
results, pointing to various threads in the mailing list.
Most helpful answers:
http://archive.ambermd.org/201211/0319.html
http://archive.ambermd.org/200701/0224.html
http://archive.ambermd.org/201208/0464.html
http://archive.ambermd.org/201208/0074.html
So, try using inp=2 and radiopt=0 in the &pb section of the MMPBSA input.
Cheers,
Jan-Philip
On 04/03/2013 09:12 AM, Albert wrote:
> Hello:
>
> I preceeded my system prmtop file with ante-MMPBS by command:
>
> ante-MMPBSA.py -p ../sys.prmtop -c ../npt4.trj -c
> complex_unsolvated.prmtop -r receptor.prmtop -l ligand.prmtop -s ':WAT'
> -n ':290'
>
>
> then I submit to MMPBSA calculation, but it failed:
>
>
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with
> /cfs/klemming/scratch/s/shuguang/install/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> mmpbsa_py_energy failed with prmtop complex_unsolvated.prmtop!
> PB Bomb in pb_aaradi(): No radius assigned for atom 11 CB 2C
>
> Exiting. All files have been retained.
>
> thank you very much
> Albert
>
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>
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Received on Wed Apr 03 2013 - 02:00:02 PDT
