[gmx-users] parameters for Cerium

Elena Molteni molteni at unisi.it
Wed Feb 26 19:12:25 CET 2003

Hi all
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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