On Mon, Apr 17, 2017, Thakur, Abhishek wrote:
>
> One more small question does it show any bond if I visualise it in
> chimera or anything? As after giving bond command I am unable to find
> any Hydrogen on Sulphur of CYS but chimera is not showing any bond.
Visualization programs differ. Use the parmed program, and its
"printBonds" command, to print out the bonds involved with any particular
atoms in your system. This explicitly shows you what is in the prmtop
file. (Many other aspects of the prmtop can also be printed, and the
"checkValidity" command can also spot some types of common errors.)
....dac
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Received on Mon Apr 17 2017 - 09:30:02 PDT
