CO3-- angle modification

User discussions
1

Hi, I’m trying to run simulations on a system with the ion CO3–. I found an article with the force field and thus I added two atoms type (C=opls_1000 and O=opls_1001) to the force field file (atomtype.atp). I modified other files: aminoacids.rtp, ffbonded.itp, ffnonbnded.itp and atomanemetype2.n2t.

I am able to create the topology, but as soon as I use grompp to genrate the fiel.tpr to use in genion I got the errors: No default angle types and No default Ryckaert-bell type.

I solved this issue by writing manually force constants in the topology file, is it right?

After that I carried on adding the cation obtaining the neutral box.

At the end of the minimization my CO3-- ion are deformed and I don’t understand why.

Can you help me please?

2

Yes, you should manually add the force constant. But it sounds like you added wrong force constants.

3

I used the constants from the attached table, but, after minimization it is like my molecule is not planar anymore.

image
image491×250 20.2 KB

The article from which I took this table is: https://dx.doi.org/10.1021/acs.jctc.0c00285

4

This is the molecule after minimization
CO3--

5

What is wrong with that geometry?

6

I expect to see the molecule perfectly planar and this does not happen

7

What kind of potential do you use for the improper dihedral? Or didn’t you add an improper at all? You shouldn’t get a complaint about RB-dihedral if you are using an proper-improper dihedral, as the parameters you post seem to suggest.

8

This is the topology I generated:

;
; File ‘topol.top’ was generated
; By user: user (1000)
; On host: Ubuntu2204
; At date: Mon Dec 16 10:31:56 2024
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-:
;
; Executable: /usr/bin/gmx
; Data prefix: /usr
; Working dir: /home/user/Documenti/Giuseppe2023/Li2CO3_Mondal
; Command line:
; gmx pdb2gmx -f CO3–_CompassII.pdb -p topol.top
; Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include “./oplsaa.ff/forcefield.itp”

[ moleculetype ]
; Name nrexcl
Other 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 CO3 rtp CO3 q -2.0
1 opls_1000 1 CO3 C1 1 1.4464 12.011
2 opls_1001 1 CO3 O1 1 -1.1488 15.9994
3 opls_1001 1 CO3 O2 1 -1.1488 15.9994
4 opls_1001 1 CO3 O3 1 -1.1488 15.9994 ; qtot -2

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 120.000 1190.00
2 1 4 1 120.000 1190.00
3 1 4 1 120.000 1190.00

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 3 4 3 180.0000 268.000 0.000000 0.000000 0.000000 0.000000

; Include Position restraint file
#ifdef POSRES
#include “posre.itp”
#endif

; Include water topology
#include “./oplsaa.ff/spce.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “./oplsaa.ff/ions.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Other 80
SOL 3684
LI 160

9

You should be using function type 1, not 3, for the dihedral.

10

I tried, but I have always the same problem: Do I have to define the improper?

11

I don’t understand your question. That line is the improper dihedral definition.

12

Sorry for not having been clear. In the ffbonded.itp, in the dihedrals sectione, I specified the dihedral (180°) and the related constant. Do I have to put define there the dihedral as improper with #define?

13

But you specify all parameter in the moleculetype, so you don’t need to modify the ffbonded.itp file at all.

14

Thus, why do you think the molecule does not stay planar?

15

As I said, you are using a type 3 dihedral instead of type 1.

16

I tried with a type 1, but I did not solve the problem. I tried with a type two and it worked.

Since the ff as I showed to you was developed for LAMMPS, do you think I need to do some changes or conversion before using it in gromacs? Could the error be due to this?

17

I think it should be a dihedral type 1 with multiplicity, the third parameter, equal to 1.

18

I tried, but I still have gemotry modification

What about the fact related to LAMMPS?

19

Ah, I didn’t check the order of the atoms. It could be that the order of the atoms doesn’t match the angle you are asking for (I haven’t checked though). If it doesn’t match, you need to swap the coordinates of two hydrogens or change the angle from 180 to 0 degrees.

20

Yes, the order of the atoms in the dihedral is certainly wrong, you put the carbon first.