[gmx-users] bad box error

[amna khan]

yes i have following this tutorial , the only difference i made is that i
didn't change the charges for ligand file.

it seems it is necessary to do this ?
am i rite ?


On Wed, Jan 30, 2013 at 1:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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