Dear users, Hope someone will answer the questions in my previous mail.
Thanks in advance, > On 6 Nov 2016, at 23:48, Qasim Pars <qasimp...@gmail.com> wrote: > > Dear users, > > I will try to do binding free energy calculation using GROMACS2016 but I am > confused a little bit about the preparation of the input files. I have a few > questions: > > 1) There are below lines to apply a harmonic distance restraint in the mdp > files of the binding free energy tutorial > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme > > pull = umbrella > pull_geometry = distance > pull_dim = Y Y Y > pull_start = no > pull_init1 = 0.654 > pull_ngroups = 1 > pull_group0 = a_1391 > pull_group1 = a_2615 > pull_k1 = 0.0 ; kJ*mol^(-1)*nm^(-2) > pull_kB1 = 4184 ; kJ*mol^(-1)*nm^(-2) > > Question 1: Instead of those lines I would like to use the [ > intermolecular_interactions ] section in the topology file with GROMACS2016. > Could you please tell me what to write the [ intermolecular_interactions ] > section? > > 2) complex.top file of the tutorial is as follows: > ; Include forcefield parameters > #include "amber99sb-ildn.ff/forcefield.itp" > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > c3 c3 0.0000 0.0000 A 3.39967e-01 4.57730e-01 > dc3 c3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 > .... > > Question 2: Why all values (sigma and epsilon) of dc3 are zero? > > [ nonbond_params ] > ; i j func sigma epsilon > c3 c3 1 3.3996700e-01 4.5773000e-01 > dc3 dc3 1 3.3996700e-01 4.5773000e-01 > .... > Question 3: Why all values of dc3 aren't zero? > > [ angle_restraints ] > ; ai aj ak al type thA kA multA thB > kB multB > 1393 1391 2615 1391 1 88.8 0.00 1 88.8 > 41.84 1 > 1391 2615 2614 2615 1 32.9 0.00 1 32.9 > 41.84 1 > > [ dihedral_restraints ] > ; ai aj ak al type phiA dphiA kA phiB > dphiB kB > 1410 1393 1391 2615 1 -159.7 0.0 0.00 -159.7 0.0 > 41.84 > 1393 1391 2615 2614 1 122.6 0.0 0.00 122.6 0.0 > 41.84 > 1391 2615 2614 2610 1 12.8 0.0 0.00 12.8 0.0 > 41.84 > ..... > Question 4: Do I still need to put those ligand parameters (dc3, [ > angle_restraints ], [ dihedral_restraints ] ... ) into the topology file to > use with GROMACS2016? > > I read section 5.4.2 and 6.1 of the GROMACS2016 manual but I couldn't > understand how to prepare the input files. > -- > Qasim Pars -- 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 gmx-users-requ...@gromacs.org.
