`No default Improper Dih. types` for ACE-PRO-NME peptide with charmm36-jul2022.ff

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No

How to reproduce an error.

What I did

I tried to execute the following command:

gmx grompp -f ions.mdp \
           -c solv.gro  \
           -p topol.top \
           -po mdout_ion.mdp \
           -o ions.tpr

but I got the error:

ERROR 1 [file topol.top, line 274]:
  No default Improper Dih. types


Excluding 3 bonded neighbours molecule type 'Protein'

Excluding 2 bonded neighbours molecule type 'SOL'

There was 1 note

-------------------------------------------------------
Program:     gmx grompp, version 2022.5
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2172)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

For more detail, I give the file error.log in the Google drive directory.

I am using charmm36-jul2022.ff.tgz and the system consists of ACE-PRO-NME.
Also, I noticed that the script succeeded in passing other amino acids and terminated normally.
This may imply proline-related issue, I suppose. But I don’t know what to fix this problem.

Could you possibly please help me to solve this issue?

Thanks in advance.

2

I found a way to work around the error, which is

Remove the line 274 in topol.top.

The line corresponds to atom ids for a dihedral angle.
When I view the atoms in PyMOL, I found them weird because a hydrogen was not connected to the other three atoms defining the dihedral angle (See the figure below):

image
image889×372 67.8 KB

Nonetheless, I don’t know why this took place… Probably, proline capped by ace and nme may not be processed normally by gmx pdb2gmx with the charmm force field, for some reason.

3

Encounter with same error for my proline rich peptide (pdb:-1CKA)
Did you find any way.

4

Unfortunately, not…

5

So I just deleted the dihedral line which cause the error
Is it correct.
Then it’s running perfectly and got the correct results
And also binding at the correct position.