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
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