Hello Pengfei,
I noticed ZN-CCCH has two different combinations.
Is there a specific scenario or situation that pertain to each of the
ZN-CCCH combinations? Or are they interchangeable?
Christy
On Jul 8, 2014 8:14 AM, "Pengfei Li" <ambermailpengfei.gmail.com> wrote:
> Hi Christy,
>
> On Jul 7, 2014, at 5:54 PM, Christy Lee <chrstl810.gmail.com> wrote:
>
> > 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?
> >
>
> Here I made a summary for the residue type combinations for each metal
> cluster in ZAFF:
> (You can also check the ZAFF.xml file for the details. )
>
> Zn-CCCC CY1 ZN1
> Zn-CCCH CY2 HE1 ZN2
> Zn-CCCH CY3 HD1 ZN3
> Zn-CCHH CY4 HD2 ZN4
> Zn-CHHH CY5 HD3 ZN5
> Zn-HHDD AP1 HE4 ZN8
> Zn-HHHD AP2 HD8 HD9 HE5 ZN9
> Zn-HHHH HDD Z10
> Zn-HHHO HD4 HD5 HE2 WT1 ZN6
> Zn-HHHO HD6 HD7 HE3 OH1 ZN7
> Zn-HHOO HDA WT2 Z11
> Zn-HOOO HE6 WT3 Z12
>
> Here the residue with HD as beginning is HID and with HE as beginning is
> HIE, with WT as beginning is water
> and with OH as beginning is hydroxyl group.
>
> > I was just wondering because in ZAFF.xml, it lists two different
> > combinations for the case of ZN-CCCH.
> >
>
> Right, the two different combinations for ZN-CCCH, one has H as HIE, and
> the other has H as HID.
> In ZAFF.xml file, you can find the first ZN-CCCH group has C as CY2 and H
> as HE1
> The second ZN-CCCH has C as CY3 and H as HD1.
>
> > Much gratitude,
> > Christy
>
> No problem. Hope it helps.
>
> All the best,
> Pengfei
>
>
> > 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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Received on Thu Jul 10 2014 - 12:00:02 PDT
