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
Received on Mon May 06 2013 - 12:00:03 PDT
