[gmx-users] MM/PBSA

[Amir Zeb]

It would be better if you follow this link for mmpbsa calculations
http://rashmikumari.github.io/g_mmpbsa/

good luck

On Aug 9, 2017 1:35 PM, "Kingsley Theras Primus Dass ." <
105726107 at gms.tcu.edu.tw> wrote:

> sure ....
> the below is my command line
> qsub /home/hauren32/Desktop/work/MM_PBSA_2.0/GMXPBSAtool/
> gmxpbsa0-1_TEST.pbs
>
> and the files i have are
> 1. npt.xtc
> 2.npt.tpr
> 2.index.ndx
> 3.topol.top
> 4. gdp.itp
> 5.protein.itp
>
>
>
>
> 2017-08-09 12:22 GMT+08:00 Amir Zeb <zebamir85 at gmail.com>:
>
> > can you please paste your command line here?
> > we can judge where you are wrong
> >
> >
> > On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." <
> > 105726107 at gms.tcu.edu.tw> wrote:
> >
> > Hi everyone,
> >
> > I am trying to calculate the binding free energy between protein and
> ligand
> > by using MM/PBSA. I included all the .itp files.  But when run the
> command,
> > am getting an error saying "NO XTC" Could someone help me, what would be
> > wrong, why such error occurs. i have pasted the error message below.
> >
> >
> > Thank you!
> >
> >
> > Select a group:
> > -------------------------------------------------------
> > Program trjconv_mpi, VERSION 4.5.5
> > Source code file: trxio.c, line: 832
> >
> > Fatal error:
> > No XTC!
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > "You Could Make More Money As a Butcher" (F. Zappa)
> >
> > Select group for least squares fit
> > Selected 27: 'complex'
> > Select group for centering
> > Selected 27: 'complex'
> > Select group for output
> > Selected 27: 'complex'
> > --
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