I follow your advice to edit the bond conditions of residues Fbg and Fen in
my rtp file. Subsequently, I should modify the hdb file to add hydrogens for
Fbg and Fen. However, I get the fatal error message " Atom +C1 not found in
residue Fbg 113, rtp entry Fbg while adding hydrogens." I can successfully
generate the structure (conf.gro) when I am using pdb2gmx command(pdb2gmx
-ff oplsaa -f 2.pdb -q -missing) with the "-missing" option and ignoring the
hdb file.
; rtp file
[ Fbg ]
[ bonds ]
C5 +C1
C5 H51
C5 H52
C5 H53
[ Fen ]
[ bonds ]
C6 -C4
C6 H11
C6 H12
C6 H13
; hdb file
Fbg 1
3 4 H C5 +C1 +C2
Fen 1
3 4 H C6 -C4 -C3
f2311-differ_residue_num.pdb
<http://gromacs.5086.n6.nabble.com/file/n5006479/f2311-differ_residue_num.pdb>
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