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
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Received on Mon May 06 2013 - 07:30:06 PDT
