[gmx-users] Grompp not finding proper dihedral

John Doe helstreak at hotmail.com
Tue Jul 29 20:45:53 CEST 2014


I'm attempting to simulate "polyethylene" using OPLS (I'm using Gromacs 5.0.1-dev).  I'm using the files from:


I have moved the OPLS force field directory to my working directory and placed "ffoplsaa.rtp" and "ffoplsaa.hdb" in the OPLS directory. I use pdb2gmx (selecting the option for OPLS in my folder) to produce the gro and top files

gmx pdb2gmx -f polyethylene.pdb -o PE_processed.gro

This works fine. I think enlarge the simulation box:

gmx editconf -f PE_processed.gro -o PE_bigBox.gro -bt cubic -c -d 2.0

Again, works fine.  I then move on to energy minimize using the mdp file from:


However, when I run grompp:

gmx grompp -f minim.mdp -c PE_bigBox.gro -p topol.top -o PE_minim.tpr

I get the following error:

ERROR 1 [file topol.top, line 162]:
  No default Proper Dih. types

ERROR 2 [file topol.top, line 163]:
  No default Proper Dih. types

ERROR 3 [file topol.top, line 164]:
  No default Proper Dih. types

ERROR 4 [file topol.top, line 165]:
  No default Proper Dih. types

ERROR 5 [file topol.top, line 166]:
  No default Proper Dih. types

I'm not quite sure why I'm getting this error because the dihedral are defined in OPLS.  Take for instance ERROR 1.  This
 error correlates to the dihedral "HC-CT-CT-CT", however, in the OPLS 
bonded parameters file, the dihedral is written out as "CT-CT-CT-HC", so
 I'm not sure why grompp is not processing this.  Does this dihedral 
need to be reversed?  Then ERROR 2 corresponds to "CT-CT-CT-CT" which is defined in the bonded parameters (file "ffbonded.itp").  So I'm not really sure what's going on.

Thanks for the help. 		 	   		  

More information about the gromacs.org_gmx-users mailing list