Hi Jan:
thanks a lot for kind advices.
The problem is still the same, here is my mmpbsa.in:
&general
startframe=960, endframe=1000, interval=5, keep_files=0,
/
&gb
igb=5, saltcon=0.150,
/
&pb
istrng=0.100, inp=2, radiopt=0,
/
best
Albert
----------------log--------------------------------------------
mmpbsa_py_energy found! Using mmpbsa_py_energy
cpptraj found! Using cpptraj
Preparing trajectories for simulation...
9 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with mmpbsa_py_energy
calculating complex contribution...
CalcError: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.
On 04/03/2013 10:30 AM, Jan-Philip Gehrcke wrote:
> 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
>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Apr 03 2013 - 02:30:02 PDT
