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
> >> > > >
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
> >> > > >
> >> > > _______________________________________________
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> >> > >
> >> > _______________________________________________
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> >> >
> >> _______________________________________________
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> >>
> >
> >
>
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Received on Thu Dec 10 2015 - 12:30:04 PST
