Dear all, I am having trouble creating topology file for simple molecule ethylene. Here is the steps. Below is the pdb file:
Ethylene.pdb: ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00 C ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00 C ATOM 3 H11 ETY 1 1.238 -0.928 0.000 1.00 0.00 H ATOM 4 H12 ETY 1 1.238 0.928 0.000 1.00 0.00 H ATOM 5 H21 ETY 1 -1.238 -0.928 0.000 1.00 0.00 H ATOM 6 H22 ETY 1 -1.238 0.928 0.000 1.00 0.00 H END Then: editconf -f Ethylene.pdb -o Ethylene.gro Ethylene.gro: 6 1ETY C1 1 0.067 -0.000 0.000 1ETY C2 2 -0.067 -0.000 0.000 1ETY H11 3 0.124 -0.093 0.000 1ETY H12 4 0.124 0.093 0.000 1ETY H21 5 -0.124 -0.093 0.000 1ETY H22 6 -0.124 0.093 0.000 0.00000 0.00000 0.00000 Then I add the following residue for ethylene to the rtp file ffoplsaa.rtp: [ ETY ] [ atoms ] C1 opls_143 -0.120 1 H11 opls_144 0.060 1 H12 opls_144 0.060 1 C2 opls_143 -0.120 2 H21 opls_144 0.060 2 H22 opls_144 0.060 2 [ bonds ] C1 H11 C1 H12 C1 C2 C2 H21 C2 H22 C2 C1 and then ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa Q1_ i dont realize what is the difference between the already created Ethylene.gro and the one in the pdb2gmx(GRO.gro). I am not getting the latter and was wondering what would be the diffrence? Q2) Below is the top file which is not generated. Once I Issue pdb2gmx, I enter "6" because pdb2gmx output says: Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermo$ 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoac$ No occupancies in Ethylene.gro Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtyp$ And finally I get a blank top file:: ; File 'Ethylene.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.4 ; ; Command line was: ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" ------------------------- output says: Select the Water Model: Reading Ethylene.gro... Read 'GROningen Mixture of Alchemy and Childrens' Stories', 6 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 1 residues with 6 atoms chain #res #atoms 1 ' ' 1 6 Reading residue database... (oplsaa) Processing chain 1 (6 atoms, 1 residues) Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. Is there something wrong with my rtp? Could I trouble you to let me know what wrong is? -- Thanks, J. N. -- 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