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, > Yun > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
