I want to simulate without building the missing residue. Does gromacs have an option of capping. I am using Gromacs 4.5.4. If not then suggest some software which I may use. Shahid nayeem
On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 17/08/2012 2:28 PM, shahid nayeem wrote: >> >> Right, I have a pdb where some of the residues are missing and when I >> try to simulate it I get LINCS warning in between the atom of the two >> ends of missing residues. So if I use a smaller time step (0.01) for >> final production run and energy minimization with setting constraint = >> none, making it computationally more expensive. Will these results >> will be O.K. > > > Does it sound OK to model missing residues with solvent (or vacuum) and have > a chemical bond between the dangling ends? It's also definitely not OK to > ignore the warning pdb2gmx gave you about this bond being too long. Plowing > ahead blindly costs more time than than being careful and painstaking. > > You need to either cap your chains or build in the missing residues with > non-GROMACS software, but what's best depends what you're trying to observe. > > Mark > > >> Shahid Nayeem >> >> On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham <mark.abra...@anu.edu.au> >> wrote: >>> >>> On 17/08/2012 2:02 PM, shahid nayeem wrote: >>>> >>>> Dear all >>>>> >>>>> One basic clarification. How does LINCS algorithm influences the >>>>> results >>>>> of final production run. In what respect a minimization, pr and final >>>>> simulation done with constraints = none and with constraint= all_bonds >>>>> are >>>>> different. >>> >>> >>> Sounds like you should do some background reading on how and why >>> constraints >>> work. Manual and refs therein are good starting points. Or your favourite >>> molecular simulation textbook. In a nutshell, you use them in production >>> simulation because they're a reasonable model and allow a larger time >>> step. >>> You might avoid them when you're not yet at equilbrium, because their >>> implementation can be brittle when your structure doesn't agree with the >>> model physics. >>> >>> Mark >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Only plain text messages are allowed! >>> * 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 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
