[gmx-users] Syntax error - File lig.prm, line 2 Last line read:

[Justin Lemkul]

On 3/10/16 9:43 AM, Nikhil Maroli wrote:
> Dear all,
> im doing protein ligand simulation i got a error whole running gmx grompp
> -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> as
>
>
> Fatal error:
> Syntax error - File lig.prm, line 2
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
>
>
> i couldt understand what was the problem in prm file.

The problem isn't in the .prm file, the problem is in the manner in which it is 
#included in your .top.

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

-Justin

> here is the links to prm ,str and mol2 file
> (prm generated using python script, and used charmgui and paramchem for
> generating required files )
>
>
>
> ligand.str
> https://drive.google.com/file/d/0BxaQk_pcR9viSWtueC1lZlBWSW8/view?usp=sharing
>
> ligand.mol2
>
> https://drive.google.com/file/d/0BxaQk_pcR9viZUtGQVlVc3djaVU/view?usp=sharing
>
> lig.prm
>
> https://drive.google.com/file/d/0BxaQk_pcR9via2ZBNjhhc1NEclE/view?usp=sharing
>
> Any suggestions welcome
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================