On 2/19/13 12:53 PM, amna khan wrote:
i generated the ligand.gro by using the command
*editconf -g my_otp_ligand.pdb -o ligand.gro*
*
*
*WARNING: all CONECT records are ignored*
*Read 38 atoms*
*No velocities found*
it printed this and after this i did as mention in tutorial
it generated the bad box error and the wc -l comand result is as follows
*and wc -l conf.gro
*
*2237 conf.gro*
*
*
*
*
*the first three lines *
*
2196
705SER N 1 -3.373 -1.131 1.295
705SER H1 2 -3.442 -1.166 1.232
705SER H2 3 -3.339 -1.043 1.261
705SER H3 4 -3.298 -1.196 1.303
and last three lines are
0_NFP HO 36 -0.376 -0.128 0.141
0_NFP C26 37 -0.328 0.137 -0.081
0_NFP C27 38 -0.293 0.373 -0.168
9.21266 2.62220 3.05500
what is woring with ligand to gro converion ?
why this bad box error arose ?
The number of atoms is wrong. The wc -l command says there are 2237 lines in
the .gro file, so subtracting three (for the title, number of atoms line, and
box vectors at the end) says you have 2234 atoms in the file. The second line
of the .gro file needs to be changed to read 2234 instead of 2196. The bad box
error arises because editconf stops reading atoms at atom 2196 and expects the
next line to be vectors, but instead finds more atoms. Again, all of this is
described in the tutorial in explicit detail; please pay very close attention to
its instructions.
-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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