Hi Justin, I have problem obtaining the structure file for the simple di atomic molecule ethylene. Below is the details of the the steps. First I used PRODRG to obtain structure of c=c=c=c as:
HETATM 1 CAA DRG 1 13.520 13.910 -14.390 1.00 20.00 C HETATM 2 CAB DRG 1 13.860 12.680 -14.670 1.00 20.00 C HETATM 3 CAC DRG 1 14.170 11.540 -14.940 1.00 20.00 C HETATM 4 CAD DRG 1 14.500 10.310 -15.220 1.00 20.00 C then I discarded the first and last lines to obtain the double bonded carbons in the middle (ethylene): HETATM 1 C2 Ethyelne 1 13.860 12.680 -14.670 1.00 20.00 C HETATM 2 C1 Ethylene 1 14.170 11.540 -14.940 1.00 20.00 C This is my Ethylene.pdb. Now I need to add the following to the rtp and hdb files. ffoplsaa.hdb: Ethylene 2 2 3 H1 C1 C2 ??? 2 3 H2 C2 C1 ??? Q 1 ) I am not sure what to enter for the last column for a di atomic molecule (C=C).? ffoplsaa.rtp: [ Ethylene ] [ atoms ] C1 opls_136 -0.120 1 H11 opls_140 0.060 1 H12 opls_140 0.060 1 C2 opls_136 -0.120 2 H21 opls_140 0.060 2 H22 opls_140 0.060 2 [ bonds ] C1 H11 C1 H12 C1 C2 C2 H21 C2 H22 C2 C1 Q 2) Also I am not sure if I need the last line which says C2 is connected to C1, given that in line 3 I have C1 C2 indicating the same thing! editconf -f Ethylene.pdb -o Ethylene.gro -bt cubic pdb2gmx -f Ethylene.gro -o Ethylene-pdb2.gro -p Ethylene-pdb2.top -ff oplsaa >& output.pdb2gmx but top file contains no information: Can you please help me with this? Thanks a lot ! ; ; ///////////////////////////////////// ; At date: ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ;; Command line was: ; pdb2gmx -f Ethylene.gro -o Ethylene-pdb2.gro -p Ethylene-pdb2.top -ff oplsaa ;; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" --------------------------------------- On 31 March 2013 12:24, Justin Lemkul <[email protected]> wrote: > > > On 3/31/13 12:23 PM, Juliette N. wrote: > >> Dear gmx users, >> >> Does anyone know how to obtain structure file for the simple ethylene >> molecule ( C-C) ? I tried PRODRG but it fails to generate structure files >> for di atomic molecules. >> >> Any suggestion is appreciated! >> >> > For something as simple as a diatomic molecule, open up your favorite text > editor and write it by hand :) > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Thanks, J. N. -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
