hello sir, Thanks for your reply. initially i tried with pdb2gmx command.but i got error. as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC. when i performed pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh
it showed error as *Processing chain 2 'A' (16 atoms, 1 residues) Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'BFC' not found in residue topology database* i know i want to include BFC residue into my rtp file but dono how to include.. how can i get those parameter to include like its angles, dihedrals etc. x2top ll give top and rtp file.so i tried that. how to solve my problem. help me with your answer sir.
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