[gmx-users] Grompp not finding proper dihedral

[Justin Lemkul]

On 7/29/14, 2:45 PM, John Doe wrote:
> Hi,
>
> I'm attempting to simulate "polyethylene" using OPLS (I'm using Gromacs 5.0.1-dev).  I'm using the files from:
>
> https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html
>
> 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:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
>
> 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.
>

Something doesn't add up.  Dihedrals can be interpreted in forward or reverse 
order, so that doesn't matter; the fact that CT-CT-CT-CT fails is indicative of 
some underlying problem with the topology.  If you can post the topology for 
download somewhere, it will be easier to diagnose.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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