[gmx-users] bad box error
amnakhan369 at gmail.com
Tue Jan 29 22:04:11 CET 2013
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
>> 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.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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