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
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 24 2013 - 08:00:02 PDT
