[gmx-users] topology

[Téletchéa Stéphane]

Le 27/02/2017 à 13:20, Dayhoff, Guy a écrit :
> I have made changes to my topol.top file.
>
> Now in my command for em.mdp I am getting 19 errors stating "NO DEFAULT
> BOND TYPE, ANGLE TYPE, ETC.”

Dear Guy,

Just to be sure, pay attention to the order of molecules in your top 
file, if your protein is before the ligand in the gro file (and waters, 
and ions, etc), the includes in your top file should match exactly the 
same order, for instance:

; Include geneic force field
#include "forcefield.itp"

; Include ligand-specific force-field
#include "ligand.itp"

HTH,

Stéphane

-- 
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
Design In Silico
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