Dear Sir
While running the following command for density.in
sander.MPI -O -i density.in -o density.out -p 3pta_DRG_solvated.prmtop -c
heat.rst -r density.rst -x density.mdcrd -ref heat.rst
It gives the following error
Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM
I did try to recover the error by following command
parmed.py -p 3pta_DRG_solvated.prmtop
loadRestrt 3pta_DRG_solvated.inpcrd
setMolecules solute_ions True
parmout 3pta_DRG_solvated1.prmtop 3pta_DRG_solvated1.inpcrd
EOF
even I tried to rectify the error using
parm outoforder.parm7
trajin outoforder.rst7
fixatomorder outprefix reorder
trajout reorder.rst7 restart
still I could not debug the error.
I request you to kindly guide me in debugging the error.
Regards
Arunima
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Received on Thu Mar 27 2014 - 00:00:03 PDT
