> On May 17, 2014, at 12:17 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com> wrote:
>
> 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 ?
Not sure. Can you post the original topology and inpcrd files so I can see what you mean? The structure should look identical. Also, did you use the "bond" command in tleap to create cross-links between previously isolated molecules? If not, you likely made a rather serious mistake when creating your prmtop file.
> 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?
You can restart from the 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) ?
The bug is still present in AmberTools 14.
> I will be thankful if someone helps me rectify the problem.
> --
> With best regards
> Kshatresh
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HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat May 17 2014 - 11:00:02 PDT
