[gmx-users] Adding ligand structure information obtained from ATB into the pdb2gmx gro file (obtained using GROMACS)

[MUSYOKA THOMMAS]

Thanks Mark,
I am now set and rolling down.
Cheers.


On Tue, Sep 10, 2013 at 11:55 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> You cannot mix the .gro and .pdb formats within the same file. One
> approach is to direct the GROMACS tool to write the output in pdb
> format simply by naming the output file with a .pdb suffix. Then you
> can do such a pasting operation, and if you've preserved the format
> correctly, proceed to use the resulting file in future GROMACS stages.
>
> Mark
>
> On Tue, Sep 10, 2013 at 11:10 AM, MUSYOKA THOMMAS
> <mutemibiochemistry at gmail.com> wrote:
> > Dear Users,
> > I am using the ATB web server to build topologies of my ligands.
> > I have tried to include the ligand UNITED ATOM STRUCTURE (generated by
> the
> > ATB) into my protein gro file generated by GROMACS by copying the
> > information in the lines starting with HETAM to the end of my protein gro
> > file and updating the number of molecules at the beginning of the file so
> > as to reflect the change.
> >
> > However, i am getting an error when i run the editconf command = Fatal
> > error: Something is wrong in the coordinate formatting of file
> > ../2oul_processed.gro. Note that gro is fixed format.
> >
> > My ligand link is =
> > http://compbio.biosci.uq.edu.au/atb/download.py?session=14360
> >
> > Can anyone tell me how to solve this.
> >
> > Thank you
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-- 
*MUSYOKA THOMMAS MUTEMI
Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
*PhD Student-Bioinformatics (Rhodes University)
*Skype ID- MUSYOKA THOMMAS MUTEMI
Alternative email - thommas at sia.co.ke
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