NEW

project

add module load gromacs/2024.2

add higrogen add if not add by and save at (unk)

then open the unk.mol2 fils add the unk or sometime otherv(UNL) . remove the ***** form the 2 line and add the unk .

Control + s

Mac: Cmd + Alt + F

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open terminal

gmx pdb2gmx -f receptor.pdb -o receptor.gro -ignh

press 1 (CHARMM36 all-atom force field)

again press 1 (TIP3P)

perl sort_mol2_bonds.pl unk.mol2 unk_fix.mol2

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https://cgenff.umaryland.edu/ or https://cgenff.silcsbio.com/

upload "unk_fix.mol2" and unk.str file is generated. save at with the name of .str

open .str file and press control A then control c and paste into notepad then save as unk.str also select all files then press save.l

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