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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> > >
> > >
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> >
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Received on Mon Nov 30 2015 - 14:00:04 PST
