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

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 8 10:44:00 CET 2005

On Tue, 2005-03-08 at 09:34 +0000, balamurugan r wrote:
> 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)" 
You have to fix this error in the pdb file first.

> 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
> bala
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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