[gmx-users] Re adding carbonate ion to the topolgy file

balamurugan r biobee at rediffmail.com
Tue Mar 8 10:34:41 CET 2005

Sir,I thank you for the suggestion and it worked.
I have added the Carbonate ion and a Fe +3 ion too. 

But i have problems again,
When i use: pdb2gmx -f 1D3K.pdb -o 1 -p top.top -n index.ndx -ignh , i get an error stating 
"Looking whether force field file ffG43a1.rtp exists 
Opening library file /usr/local/gromacs/share/top/ffG43a1.rtp
 Opening library file /usr/local/gromacs/share/top/aminoacids.dat 
Reading 1D3K.pdb...Read 'SERUM TRANSFERRIN', 2695 atoms 
Opening library file /usr/local/gromacs/share/top/xlateat.dat 
23 out of 23 lines of xlateat.dat converted succesfully 
Analyzing pdb file 
Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 331, atom 2556)" 
 and i just tried using the -merge option with pdb2gmx and again it gave me an error message:
 "Checking for duplicate atoms....
deleting duplicate atom    O  CYS2 329 ch A  pdb nr 2551
Now there are 2555 atoms
WARNING: with the -remh option the generated index file (index.ndx) might be useless (the index file is generated before hydrogens are added) 
N-terminus: NH3+ C-terminus: COO-
N- or C-terminus found this chain appears to contain no protein 
Fatal error: Atom -C not found in residue ASP1 while adding hydrogens"
I have checked all the .itp files and the changes i have made to .rtp  file. Can you please help me.
Thank you once again
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