[gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD
Peter C. Lai
pcl at uab.edu
Wed Mar 7 18:51:32 CET 2012
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
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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