Assistance Needed: "Atomtype F not found" Error in GROMACS Minimization with TFE Solvent

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1

GROMACS version:2021.4
GROMACS modification: No

Subject: Assistance Needed: “Atomtype F not found” Error in GROMACS Minimization with TFE Solvent

Dear GROMACS Community,

I am a relatively new user of GROMACS and am attempting to run my first simulation of a peptide in a water-TFE (2,2,2-trifluoroethanol) solvent mixture using the charmm36-jul2021 force field. During the energy minimization step, I encountered the following error:
text

ERROR 1 [file TFE.itp, line 23]:
Atomtype F not found

I am using pre-existing .gro and .itp files for TFE that have been successfully used in previous simulations, so I am uncertain about the cause of this error.

For reference, I am providing the contents of my TFE.gro and TFE.itp files, as well as the relevant section of my topol.top file.

TFE.gro:

PRODRG COORDS
7
1TFE F1 1 1.171 -0.007 0.589
1TFE C2 2 1.068 -0.091 0.597
1TFE F2 3 0.960 -0.033 0.547
1TFE F3 4 1.096 -0.201 0.526
1TFE C1 5 1.041 -0.128 0.744
1TFE O1 6 1.154 -0.191 0.805
1TFE H13 7 1.132 -0.212 0.901
0.52500 0.52500 0.52500

TFE.itp:

[ moleculetype ]
; Name nrexcl
TFE 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 F 1 TFE F21 1 -0.096 18.9984
2 CCl4 1 TFE C2 1 0.130 12.0110
3 F 1 TFE F22 1 -0.095 18.9984
4 F 1 TFE F23 1 -0.095 18.9984
5 CH2 1 TFE C1 1 0.174 14.0270
6 OA 1 TFE O1 1 -0.080 15.9994
7 H 1 TFE H13 1 0.062 1.0080
… (rest of the file omitted for brevity)

Relevant section of topol.top:

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

; Include water topology
#include “charmm36-jul2021.ff/tip3p.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 “charmm36-jul2021.ff/ions.itp”
#include “TFE.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
TFE 50
SOL 3765

The error appears to be related to the atomtype ‘F’ not being recognized within the force field. I would greatly appreciate any insights into resolving this issue. Additionally, if anyone has a properly parameterized TFE topology for the CHARMM36 force field or can guide me on how to obtain/create one, it would be immensely helpful.

Thank you in advance for your assistance.

Best regards,
Adrian

2

You cannot use a united-atom residue definition from a different force field and attempt to use it with CHARMM. The latest CHARMM36 port (July 2022) has TFE as an existing .rtp entry so you can automatically generate a topology for it with pdb2gmx.