[gmx-users] pdb2gmx : treat CL as C
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
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
for more information. This is a guess, because you've not told us what
It could have been that your .pdb file is badly formatted, but that
appears not to be the case here.
More information about the gromacs.org_gmx-users