Hi, Sorry I don't know how any of these non-GROMACS tools work, or even whether they actually generate Urey Bradley interactions that have all the terms. I suggest you spend some time with the documentation.
Mark On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH <[email protected]> wrote: > Sorry Mark, I failed to note that. > > I am afraid that I don't know what that are those components and how and > where to find it. If you are actually meaning about "ub0 kub" components, > how could i find the value for it. In case of swiss param generated itp > file, these components appear to be 0. Any help here please? > > > On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <[email protected]> > wrote: > > > Hi, > > > > Please read my answer. > > > > Mark > > > > On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH <[email protected]> > > wrote: > > > > > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul <[email protected]> wrote: > > > > > > > > > > > > > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote: > > > > > Dear all > > > > > > > > > > For grompp em.mdp I get an error > > > > > > > > > > ERROR 1 [file THC.itp, line 89]: > > > > > Incorrect number of parameters - found 2, expected 4 or 8 for > U-B. > > > > > > > > > > My itp file as follows > > > > > > > > > > [ angles ] > > > > > > > > > > 1 2 29 5 79.178 109.588 *{Line 89}* > > > > > 1 2 3 5 32.192 112.817 > > > > > 2 3 31 5 51.424 109.189 > > > > > > > > > > From the manual chapter 5, function of U-B is 5. And it works fine > > for > > > > > function type 2 and 8. > > > > > > > > > > Any thing better could be done? > > > > > > > > As the error tells you, the U-B functional form requires at least 4 > > > > parameters; look at its functional form. See Table 5.5. > > > > > > > > > Dear Justin > > > > > > But the parameter obtained from ffTK have only two. What could be > done.? > > > > > > > > > > > > > > > -Justin > > > > > > > > -- > > > > ================================================== > > > > > > > > Justin A. Lemkul, Ph.D. > > > > Assistant Professor > > > > Virginia Tech Department of Biochemistry > > > > > > > > 303 Engel Hall > > > > 340 West Campus Dr. > > > > Blacksburg, VA 24061 > > > > > > > > [email protected] | (540) 231-3129 > > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > > > > > > > ================================================== > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to [email protected]. > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
