Hey,
I'd like to do PB calculations for a protein using Delphi. To that end,
I'm looking for an automated way to create the Delphi charge and radius
parameter files consistent with the force field parameters I am using
for the same protein.
I've read about "delphigen" being able to read in an antechamber "ac"
file and "generate the charge and radius file for delphi calculations."
(
http://ambermd.org/antechamber/ac.html#delphigen)
Great, this is what I need... so I tried to take the following tool chain:
protein pdb file -> leap (+ force field) -> prmtop file -> antechamber
-> ac file -> delphigen -> delphi parameter files
Hence, I took the PDB file of the protein, chose a force field (ff99SB)
and created the prmtop file with leap.
But performing
antechamber -fi prepi -fo ac -i prmtop_file -o ac_file
resulted in a lot of
> the atom number exceeds the MAXATOM, reallocate memory automatically
warnings and finally yielded a segmentation fault.
According to
http://archive.ambermd.org/200905/0548.html
this is expected behavior, because antechamber is not designed to
process huge systems like entire proteins.
So for me it looks like I cannot use the indicated tool chain to perform
a "file format conversion" from prmtop to ac for big systems. Is this is
true so far? Are there other ways to automatically create delphi
parameter files consistent with the force field parameters?
Thanks a lot!
Jan-Philip
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Tue Sep 20 2011 - 03:30:02 PDT
