[gmx-users] Re: polymer duplicate atoms

[cqgzc]

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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