Hello,
My comments are below...
On Mon, Jul 19, 2010 at 4:05 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> Bill, thank you for the reply.
>
> The case of mmgbsa calculation is this. The input is a ternary complex
> which consists of protein(187 residues),peptide(12 residues) and one ligand.
> The aim is to calculate mmgbsa for this ternary complex. In this case,
> protein (A) + peptide (B) is treated as receptor while ligand (C) is treated
> as ligand itself and so simply said, [A+B] + C. Calculations showed
> reasonable values obtained from both MMPBSA.PL and MMPBSA.PY.
>
> The problem I face now is when I tried to use the same trajectory from
> [A+B] + C and aim to calculate mmgbsa for [A+C] + B, both modules of
> MMPBSA.PL and MMPBSA.PY didnt work. Using mmpbsa.pl previously, I got
> insensible numerical values.Moreover, upon using recently the mmpbsa.py, it
> wasn't able to recognize the -cp (complex prmtop) input as well as -y
> (complex mdcrd). Please be reminded that I used the same -cp and -y inputs
> for both [A+B] + C and [A+C] + B.
>
> Below is the comparison of mmpbsa.py input file. For testing, I used 50
> frames from trajectory.
>
> 1. The [A+B]+C system
>
> MMPBSA.py input file for running GB
>
> &general
>
> interval=1,
>
> verbose=2, strip_mdcrd=1,
>
> /
>
> &gb
>
> igb=2, surften=0.0072
>
> /
>
>
>
> # Execute the program
>
> $DO_PARALLEL $EXE -O -i mmpbsa.in \
>
> -sp ./ABC_solvated.prmtop \
>
> -cp ./ABC.prmtop \
>
> -rp ./AB.prmtop \
>
> -lp ./C.prmtop \
>
> -y ./ABC50f.mdcrd
> 2>>mmpbsa.out 1>>mmpbsa.out
>
>
>
> /home/biiamorasj/2011/awk/dacdif -t 3 -a 0.2
> FINAL_RESULTS_MMPBSA.dat.save FINAL_RESULTS_MMPBSA.dat
>
Why are you using dacdif here? Only tests use dacdif... it doesn't make
sense to do it for your own systems.
>
>
> 2. The [A+C]+B system
> MMPBSA.py input file for running GB
> &general
> interval=1,
> verbose=2, strip_mdcrd=1,
> receptor_mask=':1-3055 3279-3327',
>
The mask is improperly defined. These should be residue numbers, and there
should be no spaces in the masks. You should be able to remove
receptor_mask and ligand_mask from the input file, since your ligand has
continuous residues. The program will be able to figure that out on its
own, so there is no need to put it in there. If MMPBSA.py can't figure it
out, it's most likely that your prmtop files are incompatible with one
another.
ligand_mask=':3056-3278',
> # entropy=1,
> /
> &gb
> igb=2, surften=0.0072
> /
>
> # Execute the program
> $DO_PARALLEL $EXE -O -i mmpbsa.in \
> -sp ./ABC_solvated.prmtop \
> -cp ./ABC.prmtop \
> -rp ./AC.prmtop \
> -lp ./B.prmtop \
> -y ./ABC50f.mdcrd 2>>mmpbsa.out 1>>mmpbsa.out
>
> /home/biiamorasj/2011/awk/dacdif -t 3 -a 0.2 FINAL_RESULTS_MMPBSA.dat.save
> FINAL_RESULTS_MMPBSA.dat
>
> Tracing back where mmpbsa.py script knock-off, the lsf.out shows:
>
> ptraj found! Using /usr/local/amber11/bin/ptraj
> sander found! Using /usr/local/amber10_serial/amber10/bin/sander
> Assuming /usr/local/amber10_serial/amber10/bin/sander is part of
> amber9 or amber10. Using old PB input file.
> Error: Specified file (mdcrd) does not exist!
>
> And, mmpbsa.out shows:
>
> ./Run.GB: line 37: -cp: command not found
>
Are you putting spaces after the "\" at the end of each line? I believe
this will cause the error you're seeing. The "\" cancels any "special"
meaning of the next character. In this case, you want to cancel the newline
character so that it doesn't signal the end of the command. However, if you
put a space, then a newline, it cancels the space and allows the newline.
Also, you can't double-space these. It may be safer to just try and put it
all on one line to avoid this problem altogether unless you know how to
avoid it.
> My own interpretation of the error cause:
> 1. It seems to me that mmpbsa.py dont recognize the -y input mdcrd in
> [A+C]+B calculation after I implemented different numbering codes for
> receptor and ligand. What type of -y input does mmpbsa.py requires
> considering in this case I used two parts receptor.
> 2.It seems to me that the "-cp: command not found'' error flag does not
> recognize the 'ABC.prmtop' for [A+C]+B calculation.
>
This happened because it never got to the "-cp" and "-y" flags. The script
tried to interpret "-cp" as an actual command (since there must have been a
space after \ in the line before), and couldn't find an executable. It
wasn't picked up by MMPBSA.py because it wasn't on the command-line after it
(it was a new command altogether). Same thing with the -y, I'd wager.
>
> Thanks in advance for taking the time to read this post and suggestions as
> well.
> Amor
>
>
>
Hope this helps,
Jason
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 19 2010 - 08:00:03 PDT
