Dear David,
No main problem starts from here actually. I think either of antechamber
code has problem/bug. Because, even after manually editing 'ac' file
gives same error warning in prepi generation as below:
Warning: ATOM N2 has unfilled valence, assuming the linked atom name (in other residue) is "M"
change "M" to "-M" if ATOM N2 is linked to the immediate previous residue
change "M" to "+M" if ATOM N2 is linked to the immediate after residue
So, I am worrying that whether sander/pmemd code treat this molecule
nicely or not? and thats why I asked you to check with prepi file
preparation using below commnad:
prepgen -i isg_singleDouble.ac -fo prepi -o isg_singleDouble.prepi
I would also ask other Amber users/developers to make me correct or code
probably.
Many thanks,
Ashish
On Fri, 2017-06-16 at 10:54 -0400, David Case wrote:
> On Fri, Jun 16, 2017, Ashish Radadiya wrote:
> >
> > I understand about your concern and I agree that this looks unusual and
> > supposed to be carbon (7) not having valency of 5. and thats why after
> > converting this mol2 into ac file, I manually edited bond orders. I
> > suggest you to look into 'isg_singleDouble.ac'
>
> I understood you to say that everything worked fine after you did that.
> Those .ac files worked fine for me. So I'm thinking (at least for now)
> that you have solved the problem.
>
> ....dac
>
>
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Received on Fri Jun 16 2017 - 11:30:02 PDT
