Hi, I try to calculate the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond. This is the contents in the .ndx file.
[ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 17424 17425 17437 17441 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 17499 17511 17515 17523 17529 17532 17535 17536 17548 And then, I perfrom the grompp. It shows the error msg. Fatal error: atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in different energy groups How should I deal with the problem? On the other side, I read the information in the web page ( http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html) I remove the lines in the [bonds] region in .top files. But I still get these terms 1 Angle 2 G96Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Position-Rest. 13 Potential 14 Kinetic-En. 15 Total-Energy 16 Temperature 17 Pres.-DC 18 Pressure 19 Constr.-rmsd 20 Box-X 21 Box-Y 22 Box-Z 23 Volume 24 Density 25 pV 26 Enthalpy 27 Vir-XX 28 Vir-XY 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ 33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ 45 #Surf*SurfTen 46 Mu-X 47 Mu-Y 48 Mu-Z 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG 53 Coul-SR:LIG-DPPC_SOL 54 LJ-SR:LIG-DPPC_SOL 55 Coul-14:LIG-DPPC_SOL 56 LJ-14:LIG-DPPC_SOL 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC 65 Lamb-SOL 66 Lamb-LIG And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], but it is the same. Where is the wrong process? And how could I get the angle and dihedral energy in the intramolecules? Thanks for your any comments. Best, Chia-yun 2011/3/14 Mark Abraham <mark.abra...@anu.edu.au> > > > On 14/03/11, *"C.Y. Chang" * <chiayun.ch...@gmail.com> wrote: > > Hi, > > I try to calculate hydrogen bond (HB) energy. > The g_energy does not have this term. > And I find the g_hbond function in Gromacs. > But the HB energy calculation is not in g_hbond. > > > There's good reasons for this. How would you define the "HB energy" in > terms of the kind of information accessible to MD simulations? > > > Therfore, I also try to dump the .ndx file including the HB_donor, > HB_acceptor and HB_system from g_hbond, and perfrom the grompp > But there is a error msg, > > Atom 17380 in multiple Energy Mon. groups > > > Look up energy groups in the manual - start of section 3.3. Your .mdp file > is defining an illegal combination of atoms and energy monitor groups. > > > Another problem is about calculating the intramolecular energy e.g. > 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid > layer-ligand complex system. > I could set up the energy_grp and calculate energy between the ligand group > and the lipid layer group. > But I need the intramolecular energy in the groups. > How should I deal with these problems? > > > An inter-group energy doesn't mean anything much, so don't bother. Please > read the whole of this thread > http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html > > Mark > -- > 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 >
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