[gmx-users] bad box error

[Justin Lemkul]

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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