[gmx-users] regarding topology

[priya thiyagarajan]

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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