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 Thu Dec 10 2015 - 13:00:05 PST
