`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.

6

The cause of this error may come from the definition of improper torsion for ACE.

Have a look at the lines 26850-26852 (ACE’s improper torsion’s definition) in aminoacids.rtp, which says

[ impropers ]
    C   CH3    +N     O
   +N     C   +CA   +HN

The second line would be problematic if the next amino-acid is proline, because proline does not have the HN atom.

Commenting out the line causing the error could solve the issue without any unrealistic dihedral angle’s movement because the corresponding improper torsion to the deleted line has already been defined in the counterpart in the improper torsion of proline in the line 28364-28366 in `aminoacids.rtp`, which is

[ impropers ]
    N    -C    CA    CD ; <- THIS
    C    CA    +N     O

Please BE CAREFUL about believing this. I would like to be given feedback by someone.

Additional note

I also noticed that the topol.top of ACE-A-NME (NOT proline) in charmm36-jul2022.ff includes redundant pairs as follows:

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    5     1     7     6     2
    7     5     9     8     2 ; <= HERE
    7     5     9     8     2 ; <= HERE
   15     9    17    16     2
   15    19    17    16     2
   17    15    19    18     2

This indicates the unnecessary, redundant definition of the improper torsion.(Each comes from ACE and ALA)

So, my solution (deleting the line +N C +CA +HN from `aminoacids.rtp` of the charmm36-jul2022.ff) should be correct. (Indeed, amber99sb-ildn does not have +N C +CA +HN).

7

By the way, the redundancy in this case (Additional note) is not problematic, because the last definition is used as mentioned in the manual:

If parameters for a certain interaction are defined multiple times for the same combination of atom types the last definition is used; starting with GROMACS version 3.1.3 grompp generates a warning for parameter redefinitions with different values