[gmx-users] (no subject)

[Bratin Kumar Das]

Hi
    I hope there is a problem in the topology...please follow the gromacs
tutorial..

On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.biosim at gmail.com> wrote:

> Hi,
> Pls note that the maillist does not support attachments.
> Also it will better/helpful to use emails subject.
> Kind regards
> Alessandra
>
> On Tue, Nov 19, 2019 at 10:46 AM pooja kesari <poojakesari10 at gmail.com>
> wrote:
>
> > Dear All,
> > I am doing a protein-ligand simulation, when i was try to *add ions to
> the
> > system*
> > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> > *there was an error*
> > Fatal error:
> > Syntax error - File lig.prm, line 2
> > Last line read:
> > '[ bondtypes ]'
> > Invalid order for directive bondtypes
> > *my topol.top- ligand defination is as follows *
> >  ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include ligand parameters
> > #include "lig.prm"
> >
> > ; Include ligand topology
> > #include "lig.itp"
> >
> > ; Include water topology
> > #include "./charmm36-mar2019.ff/tip3p.itp"
> >
> > I have included the ligand parameter details as suggested in lig.top file
> > generated by cgenff python script. I have attached the itp and prm file
> for
> > reference.
> >
> >
> >
> > Thanks & Regards,
> > Dr. Pooja Kesari
> > Post Doctoral Fellow
> > Department Of Biosciences and Bioengineering
> > Indian Institute of Technology Bombay
> > INDIA
> > --
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