[gmx-users] (no subject)

[Alessandra Villa]

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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