GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question
I have been using GROMACS for a year now. When I run the analysis of the PDB file 5xnl, at the ‘gmx solvate’ stage after running the command line,
gmx solvate -cp 5xnl_newbox.gro -cs spc216.gro -o 5xnl_solv.gro -p topol.top
the following error message is generated
Fatal error:
String 'CHLOROPHYLL A-B BINDING PROTEIN 8, CHLOROPLASTIC; CHLOROPHYLL A-B
BINDING PROTEIN, CHLOROPLASTIC; LIGHT HARVESTING CHLOROPHYLL A/B-BINDING
PROTEIN LHCB6,; 12 CP24; PHOTOSYSTEM II PROTEIN D1; 18 PHOTOSYSTEM II Q(B)
PROTEIN; PHOTOSYSTEM II CP47 REACTION CENTER PROTEIN; PHOTOSYSTEM II CP43
REACTION CENTER PROTEIN; 28 APOPROTEIN,PROTEIN CP-43; PHOTOSYSTEM II D2
PROTEIN; CYTOCHROME B559 SUBUNIT ALPHA; CYTOCHROME B559 SUBUNIT BETA, PSBF;
PHOTOSYSTEM II REACTION CENTER PROTEIN H; 45 KDA PHOSPHOPROTEIN; PHOTOSYSTEM
II REACTION CENTER PROTEIN I, PSBI; PHOTOSYSTEM II REACTION CENTER PROTEIN J;
PHOTOSYSTEM II REACTION CENTER PROTEIN K; PHOTOSYSTEM II REACTION CENTER
PROTEIN L; PHOTOSYSTEM II REACTION CENTER PROTEIN M; OXYGEN-EVOLVING ENHANCER
PROTEIN 1, CHLOROPLASTIC; 70 II,33 KDA THYLAKOID MEMBRANE PROTEIN,OEC 33 KDA
SUBUNIT; OXYGEN-EVOLVING ENHANCER PROTEIN 2, CHLOROPLASTIC; 76 II,23 KDA
THYLAKOID MEMBRANE PROTEIN,OEC 23 KDA SUBUNIT; OXYGEN-EVOLVING ENHANCER
PROTEIN 3; LIGHT HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN LHCB4,; 83 CP29;
LIGHT HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN LHCB5,; 87 CP26; PHOTOSYSTEM
II REACTION CENTER PROTEIN T; PHOTOSYSTEM II REACTION CENTER PROTEIN W;
PHOTOSYSTEM II REACTION CENTER PROTEIN X; PHOTOSYSTEM II REACTION CENTER
PROTEIN Z’ (1273) is longer than buffer (1022).
I would like any suggestions as to what corrections I should carry out on the file to avoid this error?