Hi,
On Mon, Feb 25, 2013 at 12:57 AM, <eneas.usal.es> wrote:
> the masks). Nevertheless, when i´ve run MMPBSA.py an error related to box
> coordinates appear. Again i´ve checked the forum for solutions and i´ve
> tried to save the trajectory as crdbox. Again, this doesn´t work too...
If you post the exact error message(s) and the exact steps you took
(i.e. the input you gave to the programs) it would better help us
troubleshoot. Also, what version of AmberTools are you using, and have
all bugfixes been applied?
-Dan
>
> So, i´ve decided to split the trajectory accordingly with the coordinates
> of the receptor, ligand and no solvated complex into 3 crd files. Each one
> was then splitted into the x number of the total frames of the simulation,
> leading to x .crd files per trajectory. Then i´ve run PBSA(single point)
> and obtained VdW, EEL and PBS interaction terms. I´ve calculated the
> average of each term and molecule and the substracted to obtained the
> final interaction energies, which typicallyis E=Ecomplex-Ereceptor-Eligand
>
> My question is if this method is the same as MMPBSA.py, if not please i´ll
> apreciate any answers.
>
> Thanks a lot.
>
>
> Carlos T. Nieto
> _________________________________________________
>
> Carlos T. Nieto
> Organic Chemistry Department
> University of Salamanca
> Avda de los Caidos s/n
> 37008 Salamanca
> SPAIN
> T: 00 34 923294474
> Fax: 00 34 923294574
> email:eneas.usal.es
> _________________________________________________
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Feb 25 2013 - 07:30:02 PST
