Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.
I have a few atom types and a few atoms per each atom type. So a question - when I define interactions, say [ bonds ] can I define them by atomtype, rather that atom number?! *So like this:* [ B31 ] [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz 0.30 0 o2 oc18 -0.875 1 h2 hoy 0.350 1 o3 oc21 -0.875 1 h3 hoy 0.350 1 o4 oc17 -0.875 2 h4 hoy 0.350 2 mg1 mg 1.40 3 al1 ac3 1.35 4 o5 oc16 -0.875 5 h5 hoy 0.350 5 o6 oc20 -0.875 2 h6 hoy 0.350 2 o7 oc19 -0.875 5 h7 hoy 0.350 5 o8 oc15 -1.00 6 h8 hoz 0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex oc15 hoz b_oc-h oc16 hoy b_oc-h oc17 hoy b_oc-h oc18 hoy b_oc-h oc19 hoy b_oc-h oc20 hoy b_oc-h oc21 hoy b_oc-h ac3 oc16 a_oc-ac-h ac3 oc17 a_oc-ac-h ac3 oc18 a_oc-ac-h ac3 oc19 a_oc-ac-h ac3 oc20 a_oc-ac-h ac3 oc21 a_oc-ac-h *Rather than like this:* [ B31 ] ; [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz 0.30 0 o2 oc18 -0.875 1 h2 hoy 0.350 1 o3 oc21 -0.875 1 h3 hoy 0.350 1 o4 oc17 -0.875 2 h4 hoy 0.350 2 mg1 mg 1.40 3 al1 ac3 1.35 4 o5 oc16 -0.875 5 h5 hoy 0.350 5 o6 oc20 -0.875 2 h6 hoy 0.350 2 o7 oc19 -0.875 5 h7 hoy 0.350 5 o8 oc15 -1.00 6 h8 hoz 0.30 6 mg2 mg 1.40 7 mg3 mg 1.40 8 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h al1 o5 a_oc-ac-h al1 o4 a_oc-ac-h al1 o2 a_oc-ac-h al1 o7 a_oc-ac-h al1 o6 a_oc-ac-h al1 o3 a_oc-ac-h If I use the 1st I get .top that does not list interactions, just [ atoms ] and #include link to the FF. Is this still OK? Does it read the [ bonds ] interactions or just non bonded? Thank you, V -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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