[gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD

[Peter C. Lai]

Take a look at the entries in ions.itp for the appropriate entry format.

Note: this will probably not solve the problem of coordination bonds.

On 2012-03-07 04:49:01PM +0330, Kavosh Zandsalimi wrote:
> Dear GMX users;
>  
> I hope you are well.
> I want to simulate the interactions between DNA and Ag clusters. The problem 
> is that Amber99 ff does not know silver atoms and residues.
> I have defined Ag and Au in atomtypes.atp and assigned Ag LJ parameters in 
> ffnonbonded.itp. But I cannot find out how to define new residues.
>  
> I would be so thankful if you help me solve this problem.
>  
> ==========================================================
>  
> Kavosh Zandsalimi
> Biophysics MSc student
> Institute of Biochemistry and Biophysics(IBB),
> University of Tehran, Enghelab Ave., Tehran, Iran
> P.O. Box: 13145 - 1384

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Peter C. Lai			| University of Alabama-Birmingham
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