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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Mon Nov 30 2015 - 13:00:03 PST
