Dear Users,
I am running density equilibration of a protein ligand complex using
restart file from heating dynamics in Amber 14. During the density
equlibration I am getting an error 'Bad topology file. Sum of the atoms per
molecule does not equal.....'
Since it has been previously discussed as a tleap bug (
http://archive.ambermd.org/201308/0327.html) I followed same steps and
created fixed prmtop and inpcrd files using parmed.py. However, I have some
queries:
1.When I am loading the fixed prmtop file and fixed inpcrd files in vmd, it
shows some strange structure in vmd. Why is it so ?
2. Should I restart the simulations from initial stages
(minimization-->heating---> density) using newly created fixed prmtop file
and fixed inpcrd or should restart from heat restart file?
3. Since it is a tleap bug from previous version of AmbetTool (12, 13) will
it be continued for latest version as well (14) ?
I will be thankful if someone helps me rectify the problem.
--
With best regards
Kshatresh
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Received on Sat May 17 2014 - 09:30:02 PDT
