The mol2 file I made from the frcmod, prep and pdb file is correct. The pdb
file is what I downloaded (just changed the atom types). I use this mol2
in combination with frcmod file in tleap to build my system. Thank you so
much for all your help.
Best,
Sam
On Wed, Apr 5, 2017 at 3:17 PM, David A Case <david.case.rutgers.edu> wrote:
> 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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--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Wed Apr 05 2017 - 13:30:03 PDT
