Respected Prof. Case,
Thank you for your reply. Yes, paA has a net charge of -1.
with regards,
Saikat
On Fri, 17 May, 2019, 18:56 David A Case, <david.case.rutgers.edu> wrote:
> On Fri, May 17, 2019, Saikat Dutta chowdhury wrote:
>
> >I have isolated the lipid coordinates from the original pdb and used
> >avogadro to add hydrogens. The charge of the lipid head group is -1.
> >
> >I am using the following command for parameterization.
> >
> >antechamber -i paA-new.pdb -fi pdb -o paA.mol2 -fo mol2 -c bcc -s 2 -at
> >gaff2 -nc -1
> >
> >My question is whether I am doing it correctly as I am using the "-nc"
> flag
> >with -1?
>
> Looks OK to me: if the charge of "paA" is -1, then you need the nc flag
> you use above.
>
> ...dac
>
>
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Received on Fri May 17 2019 - 07:00:02 PDT
