[gmx-users] How to add DMSO as solvent?
Peter C. Lai
pcl at uab.edu
Wed Jun 6 00:10:15 CEST 2012
There are a number of programs that will let you build coordinates of
molecules: PRODRG, ArgusLab, VMD etc. You'll have to make sure the atom
naming and order are correct with respect to your .itp. You'll probably
have to reminimize the structure so the geometry fits the one specified
by your FF/.itp. Then you should be able to genbox.
On 2012-06-05 03:03:28PM -0700, Yun Shi wrote:
> Hello all,
> Assuming that I made my own .itp file for amber99sb-compatible DMSO
> parameters (based on Thomas Fox and Peter A. Kollman. J. Phys. Chem. B.,
> 1998, 102, 8070-8079) and included that in the .top file, how can I add
> DMSO to my system? Should I also make a .gro file in analogy to spc216.gro?
> But how?
> Thanks for any suggestion,
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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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