On Sun, Apr 10, 2011, Melanie wrote:
> Does anyone know whether I can change the bond between atoms 112 and 113
> from single to double in either leap or any other program?
Note that the Amber force fields have no concept of bond order, and hence no
distinction between single and double bonds. In some cases, they may accept
some bond order indices in certain file formats, mainly for visualization
purposes. But there may well be glitches in such "support".
> but for some reason I cannot save the
> pdb file with the atoms bonded correctly (and each with the correct
> hybridization) in Accelrys.
This sounds like a question you need to address to Accelrys. If you think
it is a problem with Amber programs, please provide details of exactly what
you did, and what the result was. A small test case is always helpful.
....dac
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Received on Sun Apr 10 2011 - 09:00:02 PDT
