[gmx-users] Topology file-residue unknown

[Juliette N.]

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.