Thanks so much Dr Vaibhav and Jason for sorting out this problem - this
is a great help for me.
Best wishes
M
On 2013/06/24 4:31 PM, Jason Swails wrote:
> On Mon, Jun 24, 2013 at 9:34 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>>
>>
>> On Mon, Jun 24, 2013 at 8:46 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote:
>>
>>> Hi, I had this problem with Amber12, which was solved by making sure that
>>> the ligand ID is included in the "print_res" option.
>>> Do let me know if you have solved it in some other way. Thanks.
>>>
>> Oh yes! I remember this (http://archive.ambermd.org/201302/0334.html <-
>> there is the thread). Thanks for the reminder. This problem is definitely
>> present here (hopefully it is the only issue). I will add a check for this
>> so there is a helpful error message. Please add residue 561 to the list of
>> printed residues in the decomp section and try running again.
>>
>> In the meantime, I will fix this.
>>
> Well it seems that I actually did fix this back in February when Dr.
> Vaibhav Dixit first brought it to my attention. If you use the latest
> version of AmberTools (version 13), this problem is already fixed. You can
> check what version of MMPBSA.py you are using with the command:
>
> MMPBSA.py --version
>
> $ MMPBSA.py --version
> MMPBSA.py: Version 13.0
>
> Your example finishes just fine for my AmberTools 13/Amber 12 installation:
>
> bash$ MMPBSA.py -O -i mmpbsa.in -o mmpbsa.dat -sp com_solvated.top -cp
> com.top -rp rec.top -lp LIG.top -y md1.mdcrd
>
> Loading and checking parameter files for compatibility...
> sander found! Using /usr/local/amber12/bin/sander
> cpptraj found! Using /usr/local/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 1 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /usr/local/amber12/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Timing:
> Total setup time: 0.114 min.
> Creating trajectories with cpptraj: 0.186 min.
> Total calculation time: 1.241 min.
>
> Total GB calculation time: 1.241 min.
>
> Statistics calculation & output writing: 0.001 min.
> Total time taken: 1.541 min.
>
>
> MMPBSA.py Finished! Thank you for using. Please cite us if you publish this
> work with this paper:
> Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke,
> H. and Roitberg, A. E.
> J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321
>
>
> All the best,
> Jason
>
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Received on Mon Jun 24 2013 - 08:00:03 PDT
