Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential only considers bonded term only. It does not contain angle,dihedral or non-bonded term. To build an ENM model the specified atom makes bond with all other atoms with certain cutoff distance. I consider the distance between two c-alpha atoms is 0.38nm and force constant of 69.1 kj/(nm)2.I have written a code which gives the number of atoms around a particular atom with in certain cut-off distance, With this i will know what are the atoms that are needed to connect a particular atom.I have generated .gro and .top files using pdb2gmx command . After generating topology file , I replace bonds section with the connectivity information i get from code. The next steps are equilibration and production. I am not sure whether it takes connectivity information from topology or not. If it is not then how can i mention it forms bonds with in certain distance . Finally , if i run the simulation with all the above mentioned steps and load the trajectory in vmd , the protien gets contracted after first step.
Thanks, Mohan On Sat, Aug 25, 2012 at 3:43 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Hi, > > In case you want the "bonds" to be dynamic I think the only way is to use > tabulated interactions. A bit tedious to set up, but doable. Note that this > will NOT emulate angles or dihedrals, just the stretching term. I can't > understand why you would want bonds between all atoms within a certain > distance, however, and I hope you know what you're doing. > > Erik > > 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: > >> Hi all, >> I want build a toplogy for a protein , for which , each and >> every atom has to make bonds with other atoms with in certain >> specified cut-off distance. How can i do this ? >> >> Please suggest me a way, >> >> >> Thanks in advance, >> Mohan >> -- >> 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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