Re: [gmx-users] general question about molecule.rtp and pdb2gmx
.rtp [bonds] requires atom names (because that's all that can be reliably deduced from the coordinate file input) .itp/.top [bonds] requires atom numbers (because prior sanity-ization is assumed) to look up the atom types to look up the interaction parameters ... and different force fields have slightly different details. Ain't life fun? Mark On Tue, Aug 27, 2013 at 6:33 PM, Justin Lemkul wrote: > > > On 8/27/13 12:30 PM, Valentina wrote: >> >> 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 hoz0.30 0 >> o2 oc18 -0.875 1 >> h2 hoy0.350 1 >> o3 oc21 -0.875 1 >> h3 hoy0.350 1 >> o4 oc17 -0.875 2 >> h4 hoy0.350 2 >> mg1 mg1.403 >> al1 ac31.35 4 >> o5 oc16 -0.875 5 >> h5 hoy0.350 5 >> o6 oc20 -0.875 2 >> h6 hoy0.350 2 >> o7 oc19 -0.875 5 >> h7 hoy0.350 5 >> o8 oc15 -1.006 >> h8 hoz0.30 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 oc16a_oc-ac-h >>ac3 oc17a_oc-ac-h >>ac3 oc18a_oc-ac-h >>ac3 oc19a_oc-ac-h >>ac3 oc20a_oc-ac-h >>ac3 oc21a_oc-ac-h >> >> *Rather than like this:* >> [ B31 ] ; >>[ atoms ] >> ; atomname atomtype charge chargegroup >> o1 oc15 -1.00 0 >> h1 hoz0.30 0 >> o2 oc18 -0.875 1 >> h2 hoy0.350 1 >> o3 oc21 -0.875 1 >> h3 hoy0.350 1 >> o4 oc17 -0.875 2 >> h4 hoy0.350 2 >> mg1 mg1.403 >> al1 ac31.35 4 >> o5 oc16 -0.875 5 >> h5 hoy0.350 5 >> o6 oc20 -0.875 2 >> h6 hoy0.350 2 >> o7 oc19 -0.875 5 >> h7 hoy0.350 5 >> o8 oc15 -1.006 >> h8 hoz0.30 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 >> > > Defining by type is ambiguous. An .rtp requires that atom names be used to > define connectivity. > > >> >> 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? >> > > No, it's not OK. In that case, you have no bonds at all, so your molecule > would go flying apart. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > > -- > gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] general question about molecule.rtp and pdb2gmx
On 8/27/13 12:30 PM, Valentina wrote: 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 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 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 oc16a_oc-ac-h ac3 oc17a_oc-ac-h ac3 oc18a_oc-ac-h ac3 oc19a_oc-ac-h ac3 oc20a_oc-ac-h ac3 oc21a_oc-ac-h *Rather than like this:* [ B31 ] ; [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 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 Defining by type is ambiguous. An .rtp requires that atom names be used to define connectivity. 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? No, it's not OK. In that case, you have no bonds at all, so your molecule would go flying apart. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] general question about molecule.rtp and pdb2gmx
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 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 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 oc16a_oc-ac-h ac3 oc17a_oc-ac-h ac3 oc18a_oc-ac-h ac3 oc19a_oc-ac-h ac3 oc20a_oc-ac-h ac3 oc21a_oc-ac-h *Rather than like this:* [ B31 ] ; [ atoms ] ; atomname atomtype charge chargegroup o1 oc15 -1.00 0 h1 hoz0.30 0 o2 oc18 -0.875 1 h2 hoy0.350 1 o3 oc21 -0.875 1 h3 hoy0.350 1 o4 oc17 -0.875 2 h4 hoy0.350 2 mg1 mg1.403 al1 ac31.35 4 o5 oc16 -0.875 5 h5 hoy0.350 5 o6 oc20 -0.875 2 h6 hoy0.350 2 o7 oc19 -0.875 5 h7 hoy0.350 5 o8 oc15 -1.006 h8 hoz0.30 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 listgmx-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
