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<BR>
Sir,I thank you for the suggestion and it worked.<BR>
I have added the Carbonate ion and a Fe +3 ion too. <BR>
<BR>
But i have problems again,<BR>
When i use: pdb2gmx -f 1D3K.pdb -o 1 -p top.top -n index.ndx -ignh , i get an error stating <BR>
"Looking whether force field file ffG43a1.rtp exists <BR>
Opening library file /usr/local/gromacs/share/top/ffG43a1.rtp<BR>
Opening library file /usr/local/gromacs/share/top/aminoacids.dat <BR>
Reading 1D3K.pdb...Read 'SERUM TRANSFERRIN', 2695 atoms <BR>
Opening library file /usr/local/gromacs/share/top/xlateat.dat <BR>
23 out of 23 lines of xlateat.dat converted succesfully <BR>
Analyzing pdb file <BR>
Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 331, atom 2556)" <BR>
and i just tried using the -merge option with pdb2gmx and again it gave me an error message:<BR>
"Checking for duplicate atoms....<BR>
deleting duplicate atom O CYS2 329 ch A pdb nr 2551<BR>
Now there are 2555 atoms<BR>
WARNING: with the -remh option the generated index file (index.ndx) might be useless (the index file is generated before hydrogens are added) <BR>
N-terminus: NH3+ C-terminus: COO-<BR>
N- or C-terminus found this chain appears to contain no protein <BR>
Fatal error: Atom -C not found in residue ASP1 while adding hydrogens"<BR>
I have checked all the .itp files and the changes i have made to .rtp file. Can you please help me.<BR>
Thank you once again<BR>
bala
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