Hi Pengfei,
I just checked the charges and you were right, thank you!
For the future reference, are there any documentations on the residue type
combinations (like CY2, HE1, ZN2 for example) to use in the case of
ZN-CCCH, ZN-CCCC, ZN-CCHH?
I was just wondering because in ZAFF.xml, it lists two different
combinations for the case of ZN-CCCH.
Much gratitude,
Christy
On Jul 7, 2014 2:05 PM, "Pengfei Li" <ambermailpengfei.gmail.com> wrote:
> Hi Christy,
>
> I also referred to that three residues: CY2, HE1 and ZN2.
>
> The data I have obtained are:
> For the CY2, the total charge is -0.53642
> For the HE1, the total charge is 0.17266
> For the ZN2, the charge is 0.43655
> So the total charge would be -0.53642*3 + 0.17266 + 0.43655 = -1.00005
>
> Can you check your data again? Thanks!
>
> All the best,
> Pengfei
>
> On Jul 7, 2014, at 1:18 PM, Christy Lee <chrstl810.gmail.com> wrote:
>
> > 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
> >>>>>> _______________________________________________
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> >>>>
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Received on Mon Jul 07 2014 - 15:00:02 PDT
