Dear all
I sincerely apologize for an inappropriate mail.
As part of modeling a polymer network I confronted with difficulty in getting force field parameters. Is there any website (or other sources) which automatically gives force field parameters (any force field, more acceptable if charmm) if we upload the .pdb, .psf files (or any topology files)?
Thank you
Jeeno Jose
Dear all
I sincerely apologize for an inappropriate mail.
As part of modeling a polymer network I confronted with difficulty in
getting force field parameters. Is there any website (or other sources)
assigning parameters or finding suitable parameters at all?
the former requires writing scripts or small programs or writing input
for tools specializing in these tasks, the latter a proper search of
the published literature.
which automatically gives force field parameters (any force field, more
acceptable if charmm) if we upload the .pdb, .psf files (or any topology
files)?
no. it cannot be done in a general way since you need additional
information about the system. all pdb based topology builders and
force field parameter assignment tools are dependent on specific
heuristics, e.g. having the pdb consist of amino acids or dna bases.
even those require manual tweaking for any "non-standard" residues.
any more general tool that works without a user providing additional
input cannot be written, since you cannot generate information that is
not there.
axel.