On 4/4/13 11:38 AM, Juliette N. wrote:
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
"C1 C2" and "C2 C1" are redundant. You don't need both.
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?
pdb2gmx produces an output coordinate file as a byproduct of its massively
complicated fix-build-process procedure.
If you're not getting the output file(s), then pdb2gmx is failing and should
produce obvious error messages.
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.
There should be more output after this line. Any reason for pdb2gmx to fail
would be printed here.
Is there something wrong with my rtp? Could I trouble you to let me know
what wrong is?
I can see nothing wrong. I was able to produce a sensible topology using all of
your input files.
-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
========================================
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