On 1/29/13 3:46 PM, amna khan wrote:
i am using the best conformation of protein ligand file obtained after
docking results
i made the .gro file by
pdb2gmx -f pro.pdb -o proceed.gro -water spc -missing -ignh
then the ligand codinates from ligand,gro was obtained from prodrug sever,
Beware the quality of PRODRG topologies - they are never sufficiently accurate
without manual reparameterization. Using the coordinates from PRODRG may or may
not cause problems. Make sure you don't allow PRODRG to run EM on the
structure, or else the docked pose will be altered.
then i pasted ligand coordinates in this file
the first three lines are
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
2059
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
last three lines are
1LIG OAR 33 0.425 -0.911 1.194
1LIG CAC 34 0.593 -1.073 1.167
1LIG CAT 35 0.500 -1.191 1.198
9.21266 2.49507 2.95990
and the output for command is
wc -l proceed.gro
2100 proceed.gro
This shows your problem. You didn't account for the fact that you pasted in a
ligand by properly incrementing the atom count on the second line of the file.
Thus, when editconf reaches atom 2059, it expects to find box vectors on the
next line, but instead finds another atom and gives you the "bad box" message.
Your file actually has 2097 atoms (2100 - 3).
Note that there is a protein-ligand tutorial available if these concepts are
unfamiliar to you.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-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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