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.
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