Likely Chimera doesn't know where to draw bonds in your ligand. E.g. if
you run some md with your prmtop and inpcrd, you will probably see the
structure being conserved.
To validate the bonding in your prmtop, try 'edit mymol' in xleap, then
you can see what amber believes to be the bonding.
Bill
On 4/14/16 12:01 AM, Sivanandam M wrote:
> Dear AMBER users,
> I am using AMBERTOOL14 for our MD
> simulation. Initially I prepared topology and coordinate file for
> ligand, receptor, and complex separately( for MM-PBSA calculation).
> After that, i added solvatebox at the distance of 9 Angstrom. Again i
> prepared, topology and coordinates for solvated complex and save as
> pdb file. I viewed pdb file Chimera. Here, the ligand molecule had
> broken and the connectivity was missing completely. we can't use this
> topology and coordinate file for our calculation. Please give your
> valuable suggestion, to find out the problem.
>
> Thank you,
>
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Received on Thu Apr 14 2016 - 01:00:03 PDT
