[gmx-users] The promblem of force field

[Mark Abraham]

On 18/02/2012 7:50 PM, xiaojiong wrote:
> Dear,
> My receptor is membrane proteins,then I get protein-ligand complex.I 
> want to do MD simulations in DPPC.I use the GROMOS96 53a6 force
> field modified in order to include Berger’s parameters for lipids .The 
> topology for the ligand was created
> employing the server PRODRG 2.5 Beta.
> When I finished the command "perl inflategro.pl system.gro 4 DPPC 14 
> system_inflated.gro 5 area.dat",
> I want to run energy minimization.I submit the command "grompp -f 
> minim.mdp -c system_inflated.gro -p topol.top -o em.tpr".The error 
> like this
> Back Off!Ijust backed up mdout.mdp to ./#mdout.mdp.4#
> Generated 813 of the 2346 non-bonded parameter combinations
> WARING 1 [file drg.itp,line1]:
> Too few parameters on line (source file toppush.c, line 1501)
>
> WARING 2 [file drg.itp,line2]:
> Too few parameters on line (source file toppush.c, line 1501)
>
> WARING 3 [file drg.itp,line17]:
> Too few parameters on line (source file toppush.c, line 1501)
>
> ERROR 1 [file drg.itp,line 21]:
> Expected a molecule type name and nrexcl

Apparently you are not following the correct file format. You'll have to 
consult chapter 5 of the manual and look at these lines and see what 
might be wrong.

>
> Program grompp, VERSION 4.5.3
> Source code file:toppush.c, line:1187
>
> Fatal error:
> Atomtype \par not found
>
> Is the force field not suitable or others?Thanks!

The formatting is wrong, but we can't tell how.

Mark