[gmx-users] Re: gold-S simulation

[francesco oteri]

Dear fatemeh,
in the topology file there is a section called [ bonds ] where the covalent
bonds are listed. You should add you bonds there. But I think modifing
specbonds.dat is easier because it allows pdb2gmx to do the "dirty" job :)

Anyway, f you have to simulate bond breaking, you can use Morse potential
whose parameters can directly derived by the armonic form. Morse potential
doesn't allow the bond breaking but the overall effect is very close!

I have to admit I never used but only read about Morse potential so I
cannot do practic advices!


Francesco


2012/12/17 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 12/17/12 4:01 PM, fatemeh ramezani wrote:
>
>>
>>
>>   Dear Justin
>>
>> According to papers, I expect gold atom interacts with the sulfur atom of
>> amino acid cysteine covalently. But in last email you said  in the case of
>> protein-Au This will not be true to add these parameters
>>   in topology file. Then in which file should I add the parameters
>> between gold and sulfur?
>>
>> What do you suggest? How do I define for the program that can be
>> established between these two atoms covalent bond ?
>>
>>
> Bonds do not break and form in standard MD.  For that, you need QM or
> QM/MM type calculations.
>
> If there should be a bond between Cys and Au, you need to write that into
> the topology or use the specbond.dat mechanism.  pdb2gmx will not create
> bonds between Au and Cys otherwise.  The other modifications you have made,
> as far as I can tell, are fine.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-- 
Cordiali saluti, Dr.Oteri Francesco