On Wed, Apr 05, 2017, Samaneh Ghassabi Kondalaji wrote:
> Thank you for your suggestion. I modified the frcmod, prep and pdb files
> (attached) by replacing any OH and HW with OK and HK atom types and
> removing all the other atom types (CT, NP, etc). This now brings me a new
> question regarding the prep file, why is one of the hydrogen atoms is
> described as an "S" while the other two as "E"? to my understanding an "E"
> atom is connected to only one other atom while the "S" one has two
> connections, Is this because the "S" one here is the first real atom in
> connection to the dummy "DU" main atoms? The same difference is observed in
> the pdb file as well.
S and E (etc.) are tree-indicators that you can mostly ignore. (If you use
the mol2 format, they don't even show up there). But be sure to check the
list of bonds in the mol2 file to make sure that you are getting the bonds you
want.
I don't understand what your PDB file looks like: this sort of connectivity
codes should not show up in that sort of file.
....dac
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Received on Wed Apr 05 2017 - 12:30:03 PDT
