Thanks Justin If I want to constrain all the bonds in the substrate molecule present inside the enzyme cavity then along with SHAKE what I need to use ?
On Fri, Nov 9, 2012 at 5:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/8/12 11:36 PM, tarak karmakar wrote: >> >> Thanks Justin >> As you see in the .mdp file I have used SHAKE. So if I want to fix >> some C-C or C-O then what algorithm I have to use ? >> > > It still doesn't make sense to me why you want to constrain only a subset of > the bonds in the system. Please explain. > > >> In my topology file I have specified following bonds to be >> constrained. The first two are covalent and the last one is M-L >> non-covalent bond. >> >> [ constraints ] >> ; index1 index2 funct length(nm) >> 6062 6063 1 0.11490000000 >> 6062 6064 1 0.11490000000 >> 6060 4309 1 0.21000000000 >> Now while implementing SHAKE it is showing >> > > This may be the source of your error. Without an explanation to the above > point, it is hard to suggest a fix. For the metal-ligand interaction, I > have already suggested two alternative approaches. > > >> Program mdrun, VERSION 4.5.5 >> Source code file: invblock.c, line: 79 >> >> Fatal error: >> Double entries in block structure. Item 5247 is in blocks 1371 and 1370 >> Cannot make an unambiguous inverse block. >> >> Please suggest me the exact protocol. > > > Please answer the above point, which I inquired about previously. > > -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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
