Error in in ions.tpr step

User discussions
1

GROMACS version:2019.1
GROMACS modification: Yes/No
Here post your question :
Hello i want to do MD for protein-ligand complex by Charmm36. I got an error about "
ERROR 13 [file ligand.itp, line 1290]:
No default Proper Dih. types"
I could not pass this error by -maxwarn option. and I found that atom type did not exist in my ligan.itp file. how i can correct this problem?

2

Hi,
to solve the problem, you can add the missing dihedral type values (function and parameters) directly in the ligand topology file.
Note function and parameters should be compatible with CHARMM36 force field.
Kind regards
Alessandra

3

Hello, thanks for your answer. how can I add this parameter manually to my topology file? I do not know each dihedral bond belong to which atom

4

Hi,
The ERROR tells you that the program does not find the parameters in the force field files for a specific dihedral [file ligand.itp, line 1290].
That allows you to identify which is the dihedral (a dihedral is defined by 4 atoms in the topology). That is the corresponding line you can add the parameters that are appropriate to define the interaction. For the syntax Table 14.
see http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table

Best regards
Alessandra

5

thanks so much for your immediate answer. i will do what you do

6

If this ligand topology was produced by CGenFF and converted using the MacKerell lab conversion script, it should have also produced a .prm file that contains any new parameters associated with the ligand. You need to #include that before the ligand topology.

7

thanks for your answer
I put ligand.prm file in topol.top. according to the protein-ligand tutorial. but again I faced an error in ions.tpr steps which could not pass with -maxwarn option. finally, I found that the dihedral option did not make correctly when I opened ligand.prm :
[ dihedraltypes ]
; ‘improper’ dihedrals
; i j k l func phi0 kphi

and I got this error when I generate ligand.str and ligand.prm
NOTE 1: Code tested with python 2.7.12. Your version: 2.7.17 (default, Sep 30 2020, 13:38:04)
[GCC 7.5.0]

NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
–Version of CGenFF detected in ligand.str : 3.0.1
–Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1

WARNING: CGenFF versions are not equivalent!

NOTE 3: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF.
============ DONE ============
Conversion complete.
The molecule topology has been written to ligand.itp
Additional parameters needed by the molecule are written to ligand.prm, which needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers, which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check
============ DONE ============

how can I correct this problem? I really thank you if you could help me with this issue

8

You need to use equivalent CGenFF versions. 3.0.1 is many years old. Use the updated ParamChem server and the latest (July 2020) C36 port to make use of CGenFF 4.4.