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" ; Include water topology #include "/charmm36.ff/tip3p.itp" ; 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 ? James 2011/10/20 James Starlight <jmsstarli...@gmail.com> > Dear, Gromac's users! > > > Today I've tried to make pure lipid bi-layer system from initial .pdb > structure with the parametrization by the charmm ff. The main goal of this > step is preparing the initial structure suitable for the futher simulation ( > creating gro, top and posre files) > > First I've download s system consisted of 72 dppc lipids solved with water. > Then I've succesfull created .gro as well as .top files by the pdb2grmx for > my lipid system. > But on futher during creatinon of the tpr file by gromp I've obtained many > errors like this > > > ERROR 4378 [file topol.top, line 83773]: > No default U-B types > > Also I've tried to make my own bi-layer by VMD membrane plugin. After > processing of this file by pdb2gmx I've obtained many .itp files like > topol_Other_chain_L2.itp included in the generated topology file topol.top. > > But during loading this structure to the grompp I've obtained above > mentioned error again. In both cases I've used mdp file for gromp consist of > minimization algorithm ( attached). > > What I've done wrong? Could you provide me with the workable algorithm for > preparation of the pure lipid system parametriezed by charm27 ? > > > Finally I have small queation about charmm structures- I've found already > pre-equilibrated bi-layers > http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb > file is accompanied by the PSF ones. As I've understood the PSF is the same > to the top in the Gromacs. Could I convert PSF to the TOP for already > pre-built system? > > > Thanks for help > > James > > James >
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