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 Mon Nov 30 2015 - 09:30:06 PST
