On Mon, 2014-03-03 at 11:06 +0000, almarques wrote:
> Hi,
>
> I have already Ambertools13 installed. When I run mmpbsa.py I obtain
> the same error as you reported
>
> Error: Atom 12403 was assigned a lower molecule # than previous atom.
> This can
> Error: happen if 1) bond information is incorrect or missing, or 2)
> if the
> Error: atom numbering in molecules is not sequential. If topology did
> not
> Error: originally contain bond info, 1) can potentially be fixed by
> Error: increasing the bondsearch cutoff offset (currently 0.200). 2)
> can be
> Error: fixed by either using the 'fixatomorder' command, or using
> Error: the 'setMolecules' command in parmed.py.
> Error: Could not determine molecule information for complex.top.
> Error: SetSolventInfo: No molecule information.
> Error: Could not determine solvent information for complex.top.
> ...
>
> but the calculation does not abort and I can get the output file with
> the energies. I don't understand the error “Atom 12403 was assigned a
> lower molecule # than previous atom” because the _MMPBSA_complex.pdb and
> the other files are correctly generated according to the masks and atom
> 12403 (the Mn atom) is correctly positioned in all the files for the
> receptor, ligand and complex. Are these errors “real errors”?
>
>
> I tried to fix the trajectory in cpptraj:
>
> parm outoforder complex.top
> trajin outoforder traj.mdcrd
> fixatomorder outprefix reorder
> trajout traj.mdcrd restart
>
> but I didn't get any output. Could someaone please tell me how to use
> the fixatomorder command to fix the whole trajectory and the
> complex.top? Should I do the same for the top files of the ligand,
> receptor and for the mutant files?
Did you type those commands into cpptraj, or were they in a script? If
you just typed them in, you need to type "go" or "run".
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 03 2014 - 05:30:02 PST
