[gmx-users] rtp topology file for ligand

[Justin Lemkul]

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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