This is what I got......
Loaded Amber topology file ../full.prmtop
Reading input from STDIN...
> > > > > Determining validity of prmtop
SyntaxError: invalid syntax (checkvalidity.py, line 19)
Loaded Amber topology file ../full.prmtop
Reading input from STDIN...
> Determining validity of prmtop
SyntaxError: invalid syntax (checkvalidity.py, line 19)
[1] + Done(1) /usr/local/amber12/bin/parmed.py -p
../full.prmtop << EOF &;;;;;checkValidity;EOF
On Mon, May 6, 2013 at 1:41 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Try this command and see what it says:
>
> parmed.py -p ../full.prmtop << EOF
> checkValidity
> EOF
>
> Does that print anything?
>
>
> On Mon, May 6, 2013 at 10:26 AM, Chinthaka Ratnaweera <cnr88.msstate.edu
> >wrote:
>
> > My input file is
> > input file for running PB and GB in serial
> > &general
> > endframe=50, keep_files=2,
> > /
> > &gb
> > igb=2, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100,
> > /
> >
> >
> >
> > On Mon, May 6, 2013 at 9:23 AM, Chinthaka Ratnaweera <cnr88.msstate.edu
> > >wrote:
> >
> > > I am getting an error when running the mmpbsa.py script.
> > > I am running the following script.
> > > /usr/local/amber12/bin/MMPBSA.py -O -i pbsa.in -o
> > > FINAL_RESULTS_MMPBSA.dat -sp ../full.prmtop -cp ../complex.prmtop -rp
> > > ../receptor.prmtop -lp ../ligand.prmtop -y ../full-equil6.mdcrd
> > > ../full-equil7.mdcrd ../full-equil8.mdcrd ../full-equil9.mdcrd
> > > ../full-equil10.mdcrd.
> > > I did the same for the previous system but did not get this error. Can
> > > anyone suggest a solution. Thank you.
> > >
> > > error msg
> > >
> > > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> > > cpptraj found! Using /usr/local/amber12/bin/cpptraj
> > > Preparing trajectories for simulation...
> > > Error: Atom 24576 was assigned a lower molecule # than previous atom.
> > > Error: This can happen if bond information is incorrect or missing.
> > > Error: Detected # of molecules is 90860. If this is incorrect and your
> > > Error: topology does not have bond information (e.g. PDB file), try
> > > Error: increasing the bond search cutoff offset (currently 0.200000).
> > > Error: e.g. 'parm full.prmtop bondsearch <new offset>'
> > > Error: Could not open parm ../full.prmtop
> > >
> > >
> > > --
> > > Chinthaka Nadun Ratnaweera
> > > Hand Lab Rm 1126
> > > Mississippi State University
> > > 310 Presidents Circle
> > > Starkville, MS 39762
> > >
> >
> >
> >
> > --
> > Chinthaka Nadun Ratnaweera
> > Hand Lab Rm 1126
> > Mississippi State University
> > 310 Presidents Circle
> > Starkville, MS 39762
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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
>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Mon May 06 2013 - 12:00:04 PDT
