Hi Vince,
Peters et al. have developed the Zinc AMBER force field (ZAFF) before (
http://pubs.acs.org/doi/abs/10.1021/ct1002626 <
http://pubs.acs.org/doi/abs/10.1021/ct1002626>).
Here is a tutorial about how to use it:
http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm <
http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm>
You can use ZAFF directly if interested.
Best,
Pengfei
> On 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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Received on Mon Nov 30 2015 - 14:00:03 PST
