I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save. 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed). Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp?
Thanks Elie > Date: Thu, 4 Oct 2012 21:25:29 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/4/12 5:56 PM, Elie M wrote: > > > > I guess the first parameter of each pair is easy to find. what about kb? k > > theta?..... kb is the force constant isnt it? any reference about a method > > how to calculate them please? pr anything atht might be of help. > > > > Bonded parameters are generally based on vibrational spectra and X-ray data. > For OPLS, the bonded parameters were originally taken from an AMBER parameter > set in the mid-1980's and have some terms have subsequently been revised over > time. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- 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
