Hi Pengfei,
I used CY2, HE1 and ZN2 from the directory you gave and still got the non
integer, -.7684.
Which cysteine, histidine and zinc were you referring to?
Thank you,
Christy
On Jul 6, 2014 9:39 AM, "Pengfei Li" <ambermailpengfei.gmail.com> wrote:
> Hi Christy,
>
> You can load the set of library under the directory
>
> $AMBERHOME/dat/mtkpp/ZAFF/201108/
>
> That one will gives you a Zn-CCCH metal site with -1 charge on it.
>
> Hope it helps,
>
> All the best,
> Pengfei
>
> On Jul 3, 2014, at 7:11 PM, Christy Lee <chrstl810.gmail.com> wrote:
>
> >
> > 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
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 07 2014 - 10:30:02 PDT
