[gmx-users] Problems with mktop 2.2.1
kiarabell at msn.com
Tue Nov 3 15:22:29 CET 2015
Dear Gromacs users,
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
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
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.
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