Without seeing your input file, I can only guess at your problem. However, I
assume the issue is that you are assuming MMPBSA.py is reading all your
trajectories as a single trajectory and using that for the start, end, and
interval variables. However, these variables are for each trajectory, not
for all the trajectories in their entirety. For example, if you have 20
trajectories with 1000 frames each and you set start=50, end=100,
interval=2, it will take every other frame starting at frame 50 and ending
at 100 for *each* trajectory. So instead of having only 25 frames, you would
actually have 25 frames x 20 trajectories = 500 frames analyzed.
My guess is that you have 200 frames or less in each of your trajectories,
which gets MMPBSA.py confused because then it is trying to take from frames
that do not exist when you tell it to start at frame 200 for each
trajectory. So you can either 1) use ptraj to combine all your trajectories
into a single trajectory before running MMPBSA.py or 2) you can use
start,end, interval in a way that better matches what you want.
I hope that helps.
-Bill
On Wed, Apr 27, 2011 at 7:52 AM, Gabriel Urquiza <urquizagabes.gmail.com>wrote:
> Dear Amberists,
>
> I've been having some hard times making MMPBSA.py understand what is it
> that
> I want to do.
> I'm using it to estimate binding free energy between an enzyme and a
> ligand,
> pretty standard
> stuff. In order to do so, I am using several trajectories in the
> expectation
> that by doing so I
> will better sample phase space and therefore will obtain more statistically
> meaningful results.
>
> However, when I tell MMPBSA.py that I want it to cut through the
> trajectories from frame 200
> to frame 20000 it will tell me this:
>
> WARNING in safe_close(): Attempting to close a NULL FILE and buffer!
>
> Beginning quasi-harmonic entropy calculation with ptraj...
> Error! Ptraj failed. Check coordinate and topology files for the complex.
>
> And when I start from frame 1 to frame 20000 it will go on and give me my
> calculations, except
> that it will take a single frame from each trajectory. Does anyone have a
> clue of what on earth is
> going on here? At first I thought it was something to do with the
> trajectories being too short, maybe
> a bug. But the interval is valid for all trajectories.
>
> Looking forward to your assistance.
>
> Gabriel
>
> ---------
> Graduation student at Federal University of Paraíba, Brazil.
> LQQC - Laboratory of Computational Quantum Chemistry
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 27 2011 - 05:30:05 PDT
