Justin, In that way there was only one point wich was not understood for me
In charmm I already have lipids.rtp with the parametries for my lipids. Also I have a single molecule of my lipid. How via pdb2gmx I could create parametrised itp file except of posre.itp ? James 2011/10/21 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> I've excluded "charmm36.ff/lipids.rtp" from my topology and obtain new >> error >> Fatal error: >> No such moleculetype POPC >> >> How I could include topology on this lipids ( all of them are present in >> the lipids.rtp. ) ? >> I have itp for the lipids only for the GROMOS ff so it should not be used >> here >> >> > I presented the details of this procedure to you already: > > http://lists.gromacs.org/**pipermail/gmx-users/2011-**October/065311.html<http://lists.gromacs.org/pipermail/gmx-users/2011-October/065311.html> > > -Justin > > >> James >> >> >> 2011/10/21 Mark Abraham <mark.abra...@anu.edu.au <mailto: >> mark.abra...@anu.edu.**au <mark.abra...@anu.edu.au>>> >> >> >> On 21/10/2011 5:41 PM, James Starlight wrote: >> >> I've also tried to make topology for my system parametriesed for >> charmm36 ff by hands but failed too :( >> >> This is my topology for the POPC bilayer wich I've made in VMD >> membrane builder as well as downloaded a pre built membrane >> system ( I've tested for both cases) >> >> ; Include chain topologies >> #include "charmm36.ff/forcefield.itp" >> >> ; Include lipids >> #include "charmm36.ff/lipids.rtp" >> >> >> .rtp files may not be #included >> >> >> >> >> ; Include water topology >> #include "/charmm36.ff/tip3p.itp" >> >> >> Initial backslash refers to the root of your file system, so is >> likely wrong. >> >> >> >> ; Include ion topologies >> #include "charmm36.ff/ions.itp" >> >> ; System specifications >> [ system ] >> 128-Lipid POPC Bilayer in water >> >> [ molecules ] >> POPC 72 >> >> When I've loaded my molecule to grompp I've obtained error >> >> Program grompp, VERSION 4.5.4 >> Source code file: /tmp/gromacs-4.5.4/src/kernel/**__toppush.c, >> >> line: 770 >> >> Fatal error: >> Unknown bond_atomtype 1 >> >> What does it means? Is here anybody who also tried to >> parametriesed theis lipids by charmm ff ? >> >> >> Don't blame the ff yet :-) >> >> Mark >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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