On 4/1/13 8:55 PM, Juliette N. wrote:
Hi Justin
I tried several residue names, 1Ethylene, 1Eth but editconf says:
Program editconf, VERSION 4.5.4
Source code file: pdbio.c, line: 446
Software inconsistency error:
Trying to deduce atomnumbers when no pdb information is present
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
What would be the correct format of pdb that is readable? Here is the pdb:
Google "PDB format."
-Justin
1Eth 1 C 0.672 -0.000 0.000
C
1Eth 2 C -0.672 -0.000 0.000
C
1Eth 3 H 1.238 -0.928 0.000
H
1Eth 4 H 1.238 0.928 0.000
H
1Eth 5 H -1.238 -0.928 0.000
H
1Eth 6 H -1.238 0.928 0.000
H
Thanks
On 1 April 2013 20:06, Justin Lemkul <[email protected]> wrote:
On 4/1/13 7:22 PM, Juliette N. wrote:
Hi all,
I am trying to produce gro file from PDB file using editconf.
Here is the pdb file
HETATM 1 C 0.672 -0.000
0.000 C
HETATM 2 C -0.672 -0.000
0.000 C
HETATM 3 H 1.238 -0.928
0.000 H
HETATM 4 H 1.238 0.928
0.000 H
HETATM 5 H -1.238 -0.928
0.000 H
HETATM 6 H -1.238 0.928
0.000 H
Then I use: editconf -f X.pdb -o X.gro
But the go file seems no to be correct
6
0 C 1 0.067 -0.000 0.000
0 C 2 -0.067 -0.000 0.000
0 H 3 0.124 -0.093 0.000
0 H 4 0.124 0.093 0.000
0 H 5 -0.124 -0.093 0.000
0 H 6 -0.124 0.093 0.000
0.00000 0.00000 0.00000
Can anyone please help why this is happening?
And what exactly is wrong with it? You have no residue numbers or names
in the input .pdb file, so none appear in the .gro file. The coordinates
have been correctly transformed from Angstrom to nm within the limit of
precision.
-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>
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========================================
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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