Dear Pengfei
Thank you so much for your suggestions.
Yes those two images are after md simulations.
As yours and Carlos suggestions I will check with parmed/xparmed method.
Again thank you so much...
Have a nice week end
Best wishes
Vince
On 12 December 2015 at 04:59, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> Hi Vince,
>
> The structures (with GB and TIP3PBOX respectively) you sent in the former
> email are structures after MD equilibration runnings, right? As Carlos
> suggested, you can use ParmEd to check the parameters about the zinc
> center. You can use printBonds, printAngles, printDihedrals and
> printDetails these commands (with each command followed by the mask of Zinc
> ion) in ParmEd to see whether the parameters related to the metal ion
> center are normal.
>
> Best,
> Pengfei
>
> > On Dec 10, 2015, at 3:34 PM, V. Kumar <vin.vasanth.gmail.com> wrote:
> >
> > Dear Carlos
> >
> > thank you so much for your response. It is the case only in pymol pdb
> view.
> > In chimera there is no bond Zn2+ apart from ligands. Even in prmtop there
> > is no bond between Zn2+ and any other atom apart from 2cys-sg and
> 2his-ne2
> > . I was wondering since Zn2+ positively charged and -COO(-), is this is
> > causing problem. Already zinc has 4 bonds with ligand residues.
> >
> > In the current ZAFF protocol, I observed that the side chain of the ASP
> in
> > particular -COO(-) group is very close to Zn2+. In my previous protocol I
> > considered Zn as an atom in ZNA residue where there was no such problem
> > with ASP side chain. This is what puzzled me. In principle my zinc
> > ordination looks fine in the current protocol, but why these ASP residues
> > are close to zinc. Where in other case not?? is it some kind of charge
> > equilibrium on the conformation.
> >
> > I will recheck my protocol...one more time..
> >
> > Again, thanks a lot.
> >
> > Have a nice day!!!
> >
> > thanks
> > Vince
> >
> > On 10 December 2015 at 21:08, Carlos Simmerling <
> carlos.simmerling.gmail.com
> >> wrote:
> >
> >> I can't help much because when you talk about "bonds" I don't know if
> you
> >> mean an actual covalent bond defined in Amber. Unless you do a QM/MM
> >> calculation, bonds in Amber are defined in the prmtop and cannot form or
> >> break during a simulation. so I don't know what you mean when you say
> you
> >> have a problem with bond formation during simulated annealing. look at
> your
> >> system prior to any simulations and check the bonds. these won't change.
> >> any problems must be fixed in the prmtop using programs like leap, they
> >> will not change during minimization or MD.
> >>
> >> if you use a visualization program that does not get bond information
> from
> >> leap (for example, using a pdb file and using distances to calculate
> bonds)
> >> then what you see as a "bond" in the graphics may or may not be an
> actual
> >> bond in Amber. you need to make sure you are examining the bonds in the
> >> prmtop. parmed can also help with this.
> >>
> >>
> >> On Thu, Dec 10, 2015 at 11:05 AM, V. Kumar <vin.vasanth.gmail.com>
> wrote:
> >>
> >>> Dear Pengfei and Dear Carlos and dear AMBER
> >>>
> >>> Good evening...
> >>>
> >>> I have managed to follow ZAFF.prep and ZAFF.frcmod (AMBER) way to
> handle
> >>> the zinc coordination.
> >>> With non-bonded model (different way to handle zinc) there was a
> problem
> >>> with CYS CYS bond formation during simulated annealing.
> >>>
> >>> I followed ZAFF.prep and ZAFF.frcmod (AMBER) as suggested by Pengfeim
> >> now
> >>> my coordination sphere is ok. But I have another problem, zinc atom is
> >>> forming
> >>> a bond with the side chain of the aspartic acid. I have neutralised my
> >>> system to net charge 0 in TIP3. Even I observed same problem in GB
> model
> >>> but when I extract
> >>> low energy structures there zinc-ASP side chain bond was absent.
> >>>
> >>>
> >>> Is this such behaviour of Zn2+ is common even after defined a 2SG-CYS
> and
> >>> 2-NE2-HIS bond during prmrop and inpcrd files generation ? I have
> >> attached
> >>> the image.
> >>>
> >>> I would highly appreciate your suggestions and ideas...
> >>>
> >>> thanks in advance ...
> >>>
> >>> Best wishes
> >>> VINCE
> >>>
> >>> PS: simulated annealing + NMR restraints on.
> >>>
> >>>
> >>>
> >>>
> >>> [image: Inline images 4][image: Inline images 3]
> >>>
> >>>
> >>>
> >>> On 1 December 2015 at 08:52, V. Kumar <vin.vasanth.gmail.com> wrote:
> >>>
> >>>> Dear Pengfei
> >>>>
> >>>> Good morning.
> >>>>
> >>>> thank you so much for your response. I will to follow tutorial link.
> >>>>
> >>>> Have a nice day..
> >>>>
> >>>> thanks a lot
> >>>> Vince
> >>>>
> >>>> On 30 November 2015 at 22:58, Carlos Simmerling <
> >>>> carlos.simmerling.gmail.com> wrote:
> >>>>
> >>>>> I don't know exactly what's going on, but if it shows the S-S bond
> >> from
> >>>>> the
> >>>>> prmtop and not the bonds to the Zn, then something went wrong. I
> think
> >>> you
> >>>>> need to read the leap output carefully, not just the "OK". read what
> >> you
> >>>>> asked it to do and any information that it wrote in response. the
> >> bonds
> >>> do
> >>>>> not seem right.
> >>>>>
> >>>>> On Mon, Nov 30, 2015 at 3:38 PM, V. Kumar <vin.vasanth.gmail.com>
> >>> wrote:
> >>>>>
> >>>>>> Dear Carlos
> >>>>>>
> >>>>>> Thanks a lot for your response.
> >>>>>>
> >>>>>> Yes I have used prmtop and inpcrd to generate that image.
> >>>>>>
> >>>>>> I followed the following procedure.
> >>>>>>
> >>>>>> First I have created a linear structure using tleap. Next I have
> >>> include
> >>>>>> the zinc metal ion information as a residue. Like Zn(atom) in
> >>>>> ZNA(residue).
> >>>>>> I took my peptide with zna residue coordinates then I bonded Zn to
> >>> 2CYS
> >>>>> and
> >>>>>> 2HIS, to save prmtop and inpcrd was not successful then I will input
> >>>>>> zinc.frcmod (the file in my first email). Then I could easily save
> >> my
> >>>>>> parmtop and inpcrd. Then I have also checked the unit in tleap, I
> >> got
> >>>>> "OK".
> >>>>>>
> >>>>>> I actually modified force field to handle zinc on my own, I found
> >>> those
> >>>>>> values on the internet.
> >>>>>>
> >>>>>> I have followed CU+ | Plastocyanin tutorial
> >>>>>> http://ambermd.org/tutorials/advanced/tutorial1_orig/section2.htm.
> >>>>>>
> >>>>>> In addition my HIS are nonstandard...
> >>>>>>
> >>>>>> As per the tutorial my procedure to generate prmtop and inpcrd with
> >> zn
> >>>>>> metal ion information is correct and I m not sure about the
> >> parameter
> >>>>> file.
> >>>>>>
> >>>>>> thanks you so much...
> >>>>>>
> >>>>>> Vince
> >>>>>>
> >>>>>>
> >>>>>> On 30 November 2015 at 18:02, Carlos Simmerling <
> >>>>>> carlos.simmerling.gmail.com
> >>>>>>> wrote:
> >>>>>>
> >>>>>>> how did you generate that picture? did it use a prmtop file for
> >> the
> >>>>>> bonds,
> >>>>>>> or distances?
> >>>>>>> are you sure that the parameters you list were used to generate
> >> your
> >>>>>>> prmtop? it doesn't seem right - you need to look carefully at the
> >>> leap
> >>>>>>> outfile file.
> >>>>>>>
> >>>>>>> On Mon, Nov 30, 2015 at 12:00 PM, V. Kumar <vin.vasanth.gmail.com
> >>>
> >>>>>> wrote:
> >>>>>>>
> >>>>>>>> Dear AMBER
> >>>>>>>>
> >>>>>>>> I have successfully complete refinement of my peptide with NMR
> >>>>>> restraints
> >>>>>>>> on. For zinc coordination I have used following parameter
> >>> (bellow).
> >>>>> In
> >>>>>>> the
> >>>>>>>> end of calculation I lost perfe tetrahedral symmetry. Two
> >> cyestein
> >>>>>>> residues
> >>>>>>>> are forming covalent bond with each other in water or
> >>>>>> C65--SH<===>SH(C68)
> >>>>>>>> about 1.5A (I have attached the image). Could any body suggest
> >> me
> >>>>> why I
> >>>>>>>> couldn't maintain proper tetrahedral geometry and why cysteins
> >>>>> forming
> >>>>>>>> covalent bonds. I am using non bonded zinc model.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> thanks you in advance...
> >>>>>>>> Vince
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> # modifications to force field for zinc finger domain
> >>>>>>>>
> >>>>>>>> my zinc coordination frcmod file...
> >>>>>>>> MASS
> >>>>>>>> ZN 65.36
> >>>>>>>>
> >>>>>>>> BOND
> >>>>>>>> NB-ZN 70.000 2.05000 #kludge by JRS
> >>>>>>>> ZN-S 70.000 2.10000 #kludge by JRS
> >>>>>>>> ZN-SH 70.000 2.90000 #for pcy
> >>>>>>>> CT-SH 222.000 1.81000 #met(aa)
> >>>>>>>>
> >>>>>>>> ANGLE
> >>>>>>>> ZN-NB-CV 50.000 126.700 #JRS estimate
> >>>>>>>> ZN-NB-CR 50.000 126.700 #JRS estimate
> >>>>>>>> ZN-NB-CP 50.000 126.700 #JRS estimate
> >>>>>>>> ZN-NB-CC 50.000 126.700 #JRS estimate
> >>>>>>>> ZN-SH-CT 50.000 120.000 #JRS estimate
> >>>>>>>> ZN-S -CT 50.000 120.000 #JRS estimate
> >>>>>>>> ZN-S -C2 50.000 120.000 #JRS estimate
> >>>>>>>> ZN-S -C3 50.000 120.000 #JRS estimate
> >>>>>>>> NB-ZN-NB 10.000 110.000 #dac estimate
> >>>>>>>> NB-ZN-SH 10.000 110.000 #dac estimate
> >>>>>>>> NB-ZN-S 10.000 110.000 #dac estimate
> >>>>>>>> SH-ZN-S 10.000 110.000 #dac estimate
> >>>>>>>> ZN-SH-CT 50.000 120.000 #JRS estimate
> >>>>>>>> CT-CT-SH 50.000 114.700 #met(aa)
> >>>>>>>> HC-CT-SH 35.000 109.500
> >>>>>>>> H1-CT-SH 35.000 109.500
> >>>>>>>> CT-SH-CT 62.000 98.900 #MET(OL)
> >>>>>>>> SH-ZN-SH 10.00 113.000 #by VK
> >>>>>>>> S-ZN-S 10.00 109.100 #by VK
> >>>>>>>>
> >>>>>>>> DIHE
> >>>>>>>> X -NB-ZN-X 1 0.000 180.000 3.000
> >>>>>>>> X -ZN-SH-X 1 0.000 180.000 3.000
> >>>>>>>> X -ZN-S -X 1 0.000 180.000 3.000
> >>>>>>>> X -CT-SH-X 3 1.000 0.000 3.000
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> NONBON
> >>>>>>>> ZN 1.10 0.0125
> >>>>>>>>
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Received on Sat Dec 12 2015 - 06:00:03 PST
