Hii,
I am trying to run MMPBSA.py, but I am getting some error like
following
*Atom 4074 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.*
So I have tried to fix it by parmed.py. In parmed.py I am getting following
messages*.*
*> pamred.py my.prmtop*
*Loaded Amber topology file my.prmtopReading input from STDIN...*
> setMolecules
Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and
ATOMS_PER_MOLECULE)
MoleculeWarning: Molecule atoms are not contiguous! I am attempting to
reorder the atoms to fix this.
ParmWarning: The atoms in my.prmtop were reordered to correct molecule
ordering. Any topology printed from now on will *not* work with the
original inpcrd or trajectory files created with this prmtop! Consider
quitting and loading a restart prior to using setMolecules
I don't know what to do next. How will I get a correct prmtop file from
parmed.py? Is it possible to change the corresponding inpcrd or rst file so
that I can produce trajectory from them. Please help.
Thanks and Regards.
Sanjib Paul
Indian Institute of Technology, Kharagpur
India
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Received on Tue Apr 26 2016 - 08:00:05 PDT
