# CO3-- angle modification **URL:** \ **Category:** User discussions\ **Created:** [December 13, 2024, 3:05pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808 "2024-12-13T15:05:28Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 13, 2024, 3:05pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/1 "2024-12-13T15:05:28Z")
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? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 9:52am UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/2 "2024-12-16T09:52:12Z")
Yes, you should manually add the force constant. But it sounds like you added wrong force constants. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 11:21am UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/3 "2024-12-16T11:21:03Z")
I used the constants from the attached table, but, after minimization it is like my molecule is not planar anymore. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/d/d935557fe429a43096fb7a56ae62ea92583fa1bd.png) The article from which I took this table is: [https://dx.doi.org/10.1021/acs.jctc.0c00285](https://dx.doi.org/10.1021/acs.jctc.0c00285) ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 11:50am UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/4 "2024-12-16T11:50:10Z")
This is the molecule after minimization ![CO3--](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c4a296c45e919417e84e836d7228395493895f97.png) ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 11:58am UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/5 "2024-12-16T11:58:20Z")
What is wrong with that geometry? ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 12:02pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/6 "2024-12-16T12:02:25Z")
I expect to see the molecule perfectly planar and this does not happen ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 1:14pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/7 "2024-12-16T13:14:27Z")
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. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 1:38pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/8 "2024-12-16T13:38:33Z")
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 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 3:39pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/9 "2024-12-16T15:39:32Z")
You should be using function type 1, not 3, for the dihedral. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 4:05pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/10 "2024-12-16T16:05:33Z")
I tried, but I have always the same problem: Do I have to define the improper? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 4:21pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/11 "2024-12-16T16:21:31Z")
I don’t understand your question. That line is the improper dihedral definition. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 4:40pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/12 "2024-12-16T16:40:32Z")
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? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 4:42pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/13 "2024-12-16T16:42:27Z")
But you specify all parameter in the moleculetype, so you don’t need to modify the ffbonded.itp file at all. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 4:49pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/14 "2024-12-16T16:49:16Z")
Thus, why do you think the molecule does not stay planar? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 8:06pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/15 "2024-12-16T20:06:29Z")
As I said, you are using a type 3 dihedral instead of type 1. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 8:33pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/16 "2024-12-16T20:33:10Z")
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? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 16, 2024, 8:41pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/17 "2024-12-16T20:41:57Z")
I think it should be a dihedral type 1 with multiplicity, the third parameter, equal to 1. ---
**Author:** ![GiuseppeP](https://avatars.discourse-cdn.com/v4/letter/g/bb73d2/32.png) [@GiuseppeP](https://gromacs.bioexcel.eu/u/GiuseppeP)\ **Post date:** [December 16, 2024, 8:44pm UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/18 "2024-12-16T20:44:00Z")
I tried, but I still have gemotry modification What about the fact related to LAMMPS? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 17, 2024, 8:06am UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/19 "2024-12-17T08:06:42Z")
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. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 17, 2024, 8:16am UTC](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808/20 "2024-12-17T08:16:34Z")
Yes, the order of the atoms in the dihedral is certainly wrong, you put the carbon first. [Next page](https://gromacs.bioexcel.eu/t/co3-angle-modification/10808.md?page=2)