[gmx-users] Problems with mktop 2.2.1

Justin Lemkul jalemkul at vt.edu
Tue Nov 3 23:14:15 CET 2015

On 11/3/15 9:22 AM, Chiara Bello wrote:
> Dear Gromacs users,
> I
>   am a student from Queen's University of Belfast, I have some problem
> using on gromacs a topology file obtained by mktop 2.2.1 and it would be great if you could help me.
> When I run this command on gromacs:
> grompp -f minim.mdp -c solvated_fivemol.gro -p topology_3.1.top -o em.tpr
> I obtain this error:
> Program grompp, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/kernel/topdirs.c, line: 146
> Fatal error:
> Invalid dihedral type 180
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Can you explain me what's it mean?What is dihedral type 180?
> I built topology file as follows:
> perl mktop_2.2.1.pl -i IBU_corrected.pdb -c charges.txt -o topology.top -ff opls -conect no
> I
>   wrote the charges.text and I set "connec no" to let mktop determine
> bonds, angles and dihedrals basing on the atomic distances in PDB.
> At the top of the topology file I changed [moleculetype] = MOL to = IBU and at the bottom I changed [molecules] = MOL to = IBU.
> I attached my files.

The list does not accept attachments.

Apparently your topology is misformatted.  grompp is finding 180 (which is 
probably a phase angle) in place of a function type.  It should be easy to spot 
because it will be obviously wrong compared to what you will find in Chapter 5 
of the manual.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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