On 12/19/12 6:02 AM, fatemeh ramezani wrote:
Dear Justin
I want exactly this, that the distance between Au-S be stable around
equilibrium value, For this purpose,Should I put the harmonic parameters
related to the gold and sulfur in ffbonded file? Or I should consider AU-S
connection as V
On 12/16/12 1:11 PM, francesco oteri wrote:
Hi fatemeh,
thank you for the references. Regarding your problem, what does it means
you don't see any interaction?
Is it possible it is just a problem of the visualization software. To be
sure, you could monitor the distance
between any S atom and th
Hi fatemeh,
thank you for the references. Regarding your problem, what does it means
you don't see any interaction?
Is it possible it is just a problem of the visualization software. To be
sure, you could monitor the distance
between any S atom and the Au atom to which it is supposed to be bound. I
hi
thanks for your attention,
all itp files are in OPLSAA forcefield folder that I attached it for you.
Fatemeh Ramezani
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Dear francesco
I extract gold parameter from papers that I attached them for you. But for
gold and other atom parameters, you should calculate them using common
combination rule.
Fatemeh Ramezani
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Hi fatemeh,
I am looking for prameters like yours, where have you took the parameters
for gold and gold-aminoacid inteaction?
Francesco
2012/12/16 Peter C. Lai
> Where is the .itp file for the system?
>
> On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
> > hi
> >
> >
> > I'm simulating
Where is the .itp file for the system?
On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
> hi
>
>
> I'm simulating gold atom interaction with aminoacidcys. I have made
> gold-cys.pdb by hyperchem software:
>
> HETATM 1 N CYS 1 0.000 1.335 0.000
> HETATM 2 CA CY
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