Can you send me full.prmtop off-list?
Thanks,
Jason
On Mon, May 6, 2013 at 2:53 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> 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
> _______________________________________________
> 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
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Received on Mon May 06 2013 - 13:30:02 PDT
