AMBER Archive (2006)
Subject: RE: AMBER: Parmchk problems (parm99.dat)
From: Prashanth Athri (athriprashanth_at_yahoo.com)
I still have some questions about this .
Junmei Wang <jwang_at_encysive.com> wrote:Message If one assigns AMBER atom types (in uppercase) and wants to borrow parameters from gaff (all atom types in lowercase), one needs to combine amber protein/nucleic acid force field with gaff for parmchk work properly. Here I attached the combined parm99/gaff parameter file with this email. Since I placed amber parameters before the gaff parameters for each section (element, bond length, bond angle, torsional angle, improper torsional angle, vdw). Amber force field parameters are first considered by parmchk to assign substitutes for the missing parameters.
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Prashanth Athri
Thanks for the reply-- here are the files.
In the .frcmod file, theree are a lot of parameters that are already parameterized in the parm99.dat file. (using Amber 8)
Junmei Wang <jwang_at_encysive.com> wrote: Please attach the trouble molecules. I tested parmchk with phenol by using similar commands you used and it works fine.
[I have tried to use the most updated antechamber as suggested by previous threads....this gives the same problem.]
When I run use
Now, when I run
The output does not reflect the parameters that are present in parm99.dat. Instead most parameters are shown to be missing(all values are zerous, i.e the ff params). Is there anything obviously wrong in what I am doing?
I am trying to some dihedral calculations on benzimidazole- phenyl system. This problem is with respect to the benzimidazole, which has a five membered ring very similar to the Ade, Gua systems, hence the use of parm99.dat
Ofcourse I can manually change every value, does anyone have other suggestions? Thx in advance.