ZAFF.prep
<
https://docs.google.com/file/d/0B9GWOTD3JI6DaHFaR0VtUWN5VzNNWXNfdEk4WnNmY1VSWHlV/edit?usp=drive_web>
ZAFF.frcmod
<
https://docs.google.com/file/d/0B9GWOTD3JI6DX3FlTDhuY3RKbDF4OVlFQVZDTVdCMGxaYnZz/edit?usp=drive_web>
mcpb.bcl
<
https://docs.google.com/file/d/0B9GWOTD3JI6DVmh4R3ZaM0dYWnJkU2ZNX3NrendzcnhIcEU4/edit?usp=drive_web>
MCPB.log
<
https://docs.google.com/file/d/0B9GWOTD3JI6DNEV6cDYwV3RmZ2hNcEk4WTJsamF3S3R3bnRn/edit?usp=drive_web>
Hi Pengfei,
I used this command:
MCPB -i mcpb.bcl -l MCPB.log
and I have attached these files here.
I have also attached frcmod and prep file; hoping that it would help.
Thank you,
Christy
On Wed, Jul 2, 2014 at 2:12 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Christy,
>
> How did you do the charge fitting? Can you send me the input file for the
> charge
> fitting step you did by using MCPB?
>
> All the best,
> Pengfei
>
> On Jul 2, 2014, at 5:07 PM, Christy Lee <chrstl810.gmail.com> wrote:
>
> > Hello
> >
> > We used MCPB for the ZAFF parameter.
> > I can see from
> >
> $AMBERHOME/AmberTools/examples/mtkpp/MCPB/CCCH-2GIV/data/2GIV_large_mk.log
> > file that histidine was treated as neutral.
> > However, the resulting charge of the local system comes out to be a non
> > integer.
> > It has the charge of -.7684
> >
> > Thank you,
> > Christy
> >
> > Hello Christy,
> >
> > Where did you get the ZAFF parameters?
> >
> > I checked the
> >
> $AMBERHOME/AmberTools/examples/mtkpp/MCPB/CCCH-2GIV/data/2GIV_large_mk.log
> > file,
> > , which is the RESP charge output gaussian file of the CCCH system. and
> > found the total charge of the system is -1,
> > which shows it treats the Histidine as neutral.
> >
> > All the best,
> > Pengfei
> >
> > On Jul 1, 2014, at 5:00 PM, Christy Lee <chrstl810.gmail.com> wrote:
> >
> >> Hello AMBER users,
> >>
> >> We used ZAFF parameters for ZN interacting with three cysteines and one
> >> histidine.
> >> The expected charge of the local system is neutral:
> > (Zn+2)(C-)(C-)(C-)(H+).
> >> However, we have histidine with a neutral charge.
> >> What could be the problem?
> >>
> >>
> >> Thank you,
> >> Christy
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Received on Thu Jul 03 2014 - 16:30:02 PDT
