[gmx-users] pdb2gmx : treat CL as C

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 17 06:31:43 CET 2009

Nilesh Dhumal wrote:
> this is the command,
> pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
> Here I have attached the dioxin.pdb file.
> IN di.pbd there is no CL atoms.

I asked for your inputs and outputs. You haven't told me which 
forcefield you input or anything about what pdb2gmx wrote as output to 
the terminal.

People on this list have better things to do than guess about your 
problems, and read about other people's guesses. Already two other 
people have provided guesses that I don't think are near to solving the 
real problem. Hundreds of people have now wasted their time receiving 
and/or reading those :-) If you provide more information, people are 
more willing to help and can do it better. See 

Your pdb2gmx procedure can't work unless you've included dioxin in your 
force field's .rtp file. That's more work than just writing an .itp file 
by hand, or generating one from another mechanism. See 
http://www.gromacs.org/Documentation/File_Formats/Topology_File and 
for more information. This is a guess, because you've not told us what 
you're doing.

It could have been that your .pdb file is badly formatted, but that 
appears not to be the case here.


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