On Fri, 30 Oct 2009 18:04:43 -0400, Tom Joseph <ttjoseph.gmail.com> wrote:
>> First question : what is CN1, I suppose a program internal variable?
>
> Yes, cn1, cn2, et cetera are variables in the source code. Even if you
> don't know Fortran, you can look at rdparm.f for clues about what
> variable name corresponds to what block type - e.g.
> LENNARD_JONES_ACOEF, BOND_FORCE_CONSTANT are (relatively) easy to
> figure out. Some of the other ones, however, are a bit more opaque.
>
>> The number of atom types are respective to the forcefield or only
>> respective to the current structure?
>
> They are with respect to that particular prmtop file.
>
>> Where can I find all the input files for reading the atom type indices,
>> CN1, CN2, ASOL, BSOL for the amber 99 ff?
>
> These are assembled from the force field files in
> $AMBERHOME/dat/leap/. See, for example, leaprc.ff99 to see exactly
> which files it reads. Once the prmtop and inpcrd are created you don't
> need any other files to get all the parameters you need for that
> particular simulation.
Thanks for the answer. Inherent question : The A & B coefficients are then
given as a matrix of NTYPES x NTYPES, ntypes being the number of distinct
atom types that exist in the system. They are sorted in increasing order in
this matrix that is present in the prmtop file?
Best regards
Peter
>
> --Tom
>
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--
Peter Schmidtke
----------------------
PhD Student at the Molecular Modeling and Bioinformatics Group
Dep. Physical Chemistry
Faculty of Pharmacy
University of Barcelona
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Received on Fri Oct 30 2009 - 17:30:02 PDT
