GROMACS version: 2021.3
GROMACS modification: Yes
Hi,
I am trying to do a relative binding energy w/ ligand modification. The ligand is a short peptide, and I have put the non-canonical amino acid into the FF. The non-canonical amino acid is trifluoromethyl-phenylalanine.
I am using a modified amber99sb FF. I have modified aminoacids.rtp (and.hdb), atomtypes, nonbonded, and bonded, all to include F3 of the trifluoromethyl group. I will put some of the lines below for context:
aminoacids.rtp:
[ TFP ] ; 4-(Trifluoromethyl)-phenylalanine
[ atoms ]
N N -0.4700 1
H H 0.3100 2
CA CT 0.0700 3
HA H1 0.0900 4
CB CT -0.1800 5
HB1 HC 0.0900 6
HB2 HC 0.0900 7
CG CA 0.0000 8
CD1 CA -0.1150 9
HD1 HA 0.1150 10
CD2 CA -0.1150 11
HD2 HA 0.1150 12
CE1 CA -0.1150 13
HE1 HA 0.1150 14
CE2 CA -0.1150 15
HE2 HA 0.1150 16
CZ CA -0.1400 17
CH CF3 1.1600 18
FH1 F3 -0.3400 19
FH2 F3 -0.3400 20
FH3 F3 -0.3400 21
atomtypes.atp:
F3 18.99800 ; fluorine, trifluoro
ffbonded.itp:
[ bondtypes ]
CT F3 1 0.13600 361990.5
[ angletypes ]
F3 CT F3 1 106.0810 986.42
CA CT F3 1 112.2780 693.14
[ dihedraltypes ]
| F3| CT| CA|CA| 9| 0.00| 0.4184| 3
ffnonbonded.itp:
[ atomtypes ]
F3 9 18.99800 0.000 A 0.2850875898 0.405848
[ pairtypes ]
CT F3 1 0.311814551349 0.130309939452
lig.top (this is how I have described the atom in the topology):
176 F3 150 TFP FH1 176 -0.34 18.998 MCH3 0.000000 18.9888
177 F3 150 TFP FH2 177 -0.34 18.998 MCH3 0.000000 18.9888
178 F3 150 TFP FH3 178 -0.34 18.998 MCH3 0.000000 18.9888
I can solvate the molecule, but as soon as I try the following prompt, I get the following response:
Command line:
gmx grompp -f tests/ions.mdp -po tests/ions.out.mdp -c tests/lig_solvated.gro -p tests/lig.top -o tests/lig_ions.tpr -maxwarn 1Setting the LD random seed to 2122252150
Generated 2145 of the 2145 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5Generated 2145 of the 2145 1-4 parameter combinations
ERROR 1 [file lig.top, line 214]:
Atomtype F3 not found
Program: gmx grompp, version 2021.3-MODIFIED
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1409)
I don’t understand why this atom type can’t be found, I thought I had described it in all the relevant fields. Thank you in advance for your help.