[gmx-users] parameters for Cerium
molteni at unisi.it
Wed Feb 26 19:12:25 CET 2003
I am trying to perform a minimization (using gromacs) on a peptide with
Cerium(III) linked to it. Which can be a reasonable way to obtain/choose
parameters for Ce(III)? So far I have run pdb2gmx, to generate the
topology, adding an atom type and a residue type "CE3+", respectively, to
the .atp and .rtp files in my gromacs directory (the only information
needed seems to be the charge and atomic weight, if I'm not wrong), but now
I have to run grompp to prepare the input for minimization and, of course,
at this stage the program doesn't find "CE3+". I think it needs the VdW
parameters in the ....nb.itp file, but ... there are two problems:
1) in this ...itp file I expected to find just one list of atom types with
their respective VdW parameters, but instead there are several lists...
what is their meaning?
2) anyway, how can I obtain reasonably good VdW "c6" and "c12" parameters
for Ce(III)? (without running an ab initio calculation or something like
that!) Which is their exact definition? (I know the general form of the VdW
potential, but I remember there are slightly different definitions...). Can
I find some information on this on the gromacs website or somewhere else?
Thanks in advance
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