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:
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