[gmx-users] Problem with energy min. in membrane tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon May 4 21:51:22 CEST 2009

Ragnarok sdf wrote:
> Hello, I was following the steps in Justin Lemkul's tutorial for
> insertion of a protein in a lipid bilayer and have come accross a
> problem right after using inflategro's script from Tieleman's website.
> It says there that I should run an energy minimization and then
> continue with the steps of the tutorial. Well, I have used the output
> structure from inflategro to run an energy minimisation using
> grompp/mdrun using a steepest descent algorithm. The problem is that
> when I type the command:
> grompp -f em_steep.mdp -c inflatedbilayer.gro -p topol.top -o
> inflatedbilayer.tpr
> The following errors appear:
> ERROR 1 [file topol.top, line 523]:
>   No default G96Angle types
> ERROR 2 [file topol.top, line 794]:
>   No default Proper Dih. types

So what are on these lines?  If you can identify which atoms these correspond 
to, you will be able to determine whether or not parameters for this angle and 
dihedral actually exist within the force field.


> It seems that I have made some mistake with the forcefield's parameter
> files, but I have tried to do everything all over again and the same
> errors occur.
> Has anyone had any similar problem?
> I would appreciate some help if possible.
> Thank you
> Fabrício Bracht
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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