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 Tue Dec 01 2015 - 00:00:05 PST
