hello sir, i dono what i did was correct or not. But i did it. please tell me what i did was correct or not,, i tried two different ways to generate my top file.
first i did prodrg for my whole lipopeptide and got its itp . pdb and gro file. then i included information about atomtype, bond, pairs ,dihedrals from this prodrg.itp into charmm27 forcefield rtp. And also added DRG as lipid in residuetype.dat.. then i tried *pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh* but i got error as * No atom found in .rtp file in residue moleculetype.* so i though of using pdb file obtained from prodrg as input and repeated the step. But still i am getting the same error. second way i took one topology file generated for some protein and edited it. and i included my prodrg.itp file using include mechanism then set box to that prodrg.gro file and added water. And used that top file which i edited since it contain all information about my pdb. even my SOL molecules got written in that topology file. then i viewed that proteinwater.pdb file using pymol. when i go for energy minimisation i got error *atomtye CH3 not found*. please help me with your answer.. Thanking you,
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