Modified aminoacid

GROMACS version: 2021.5
GROMACS modification: No
Forcefield: Charmm 36m


I’m trying to simulate a modified aminoacid using the Charmm 36m force field, since there are no parameters for this aminoacid in the charmm force field I used the Cgenff webserver to generate the topology of my molecule and used the information in the generated .str file to modify my ffbonded.itp. Note that I had to edit the ffbonded file since there were no angle types nor dihedral types for the bonds in my molecule (I tried running the simulation without this modification, it didn’t work). After I made these modifications the simulation worked, but after I performed the energy minimization I noticed that my molecule that should be planar, was bent in an odd way.

This is how it looks like after performing an energy minimization:

Screenshot from 2022-10-27 23-10-53

I spent the last couple days modifying parameters in the ffbonded file and was able to narrow it down to this pointed with an arrow.

 9270    NG2S0    CG2O1   CG2R61   CG2R61     9   1.0000000        180.00     2 ; <==== Error cause
 9271   CG2R61    CG2O1    NG2S0    CG2O1     9   1.8400000          0.00     1 ;! /tmp/php , from CG2R61 CG2O1 NG2S1 CG2O6, penalty= 13.5
 9272   CG2R61    CG2O1    NG2S0    CG2O1     9   1.0100000        180.00     2 ;! /tmp/php , from CG2R61 CG2O1 NG2S1 CG2O6, penalty= 13.5
 9273   CG2R61    CG2O1    NG2S0    CG311     9   1.6000000          0.00     1 ;! /tmp/php , from CG2R61 CG2O1 NG2S1 CG321, penalty= 10.6
 9274   CG2R61    CG2O1    NG2S0    CG311     9   4.0000000        180.00     2 ;! /tmp/php , from CG2R61 CG2O1 NG2S1 CG321, penalty= 10.6
 9275    OG2D1    CG2O1    NG2S0    CG2O1     9   0.5800000        180.00     2 ;! /tmp/php , from OG2D1 CG2O1 NG2S1 CG2O6, penalty= 13.5
 9276    OG2D1    CG2O4    CG311    NG2S0     9   0.0000000          0.00     1 ;! /tmp/php , from OG2D1 CG2O4 CG311 NG2S1, penalty= 1
 9277    HGR52    CG2O4    CG311    NG2S0     9   0.0000000        180.00     3 ;! /tmp/php , from HGR52 CG2O4 CG311 NG2S1, penalty= 1
 9278    CG2O4    CG311    NG2S0    CG2O1     9   0.2000000        180.00     1 ;! /tmp/php , from CG2O1 CG311 NG2S0 CG2O1, penalty= 3

If I modified this dihedral from 180.000 to 0.0000 the rings would remain planar even after the energy minimization. But I was specifically told that I cannot simply modify the generated parameters.

all my files can be found at this github repository: GitHub - T98G/Naphtahalimide

Please I really need help, I don’t know what else to do so I came here

This is what it should have looked like

Screenshot from 2022-10-27 23-11-50

You can check whether the angle between the two planes defined in this improper is 180 or not since no one except you knows the atomnames.

A dihedral with 2-fold multiplicity and a phase angle of 180 has an energy minimum at 0 (cis), which is the desired behavior. You may have atoms in a different order (coordinates vs. topology), which should be printed in an obvious warning by grompp or you may have angles that do not sum to the appropriate value around planar centers, which causes distortion.

Thank you for your reply, I’m going to try that

Thank you for your reply. I haven’t got any warning from grompp. So it’s probably the angles that don’t sum up to the right value, right? But, I’m not sure about how to fix it, I got these parameters from CGenff, I’ve only been doing molecular dynamics for a couple months.

It’s only one possibility. I’ve seen this issue many times on the forum, so it would be in your interest to look up previous threads. That molecule is really distorted; I suspect something more fundamentally wrong is at play here. But I can’t say based on snapshots alone.

Thank you, I’m going to look up the previous threads