AMBER Archive (2006)

Subject: RE: AMBER: Parmchk problems (parm99.dat)

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Wed Sep 20 2006 - 22:46:19 CDT

Hi Junmei
How this uppercase vs lowercase recognition is done under cygwin?
My feeling is that cygwin does not recognize the difference,
and it could be the problems.

Piotr

On Tue, 12 Sep 2006, Junmei Wang wrote:

> Date: Tue, 12 Sep 2006 13:41:21 -0500
> From: Junmei Wang <jwang_at_encysive.com>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Parmchk problems (parm99.dat)
>
> 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.
>
> Now one can run the following command to get additional force field
> parameter file
>
> parmchk -i input.mol2 -f mol2 -o missing_parm.frcmod -p
> parm_for_parmchk.dat
>
> All the best
>
> Junmei
>
>
>
>
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Prashanth Athri
> Sent: Tuesday, September 12, 2006 10:54 AM
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Parmchk problems (parm99.dat)
>
>
>
> Thanks for the reply-- here are the files.
> I have attached a copy of the parm99.dat file that I use as
> well.
>
> 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.
>
> All the best
>
> Junmei
>
>
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Prashanth Athri
> Sent: Sunday, September 10, 2006 7:23 PM
> To: amber_at_scripps.edu
> Subject: AMBER: Parmchk problems (parm99.dat)
>
>
>
> Dear users:
>
> [I have tried to use the most updated
> antechamber as suggested by previous threads....this gives the same
> problem.]
>
> When I run use
> "antechamber -at amber ......"
> the output has amber atomtypes (as expected)
>
> Now, when I run
> "parmchk -p $AMBERHOME/dat/leap/parm/parm99.dat
> -i antechamber_output.mol2 -f mol2 -o missing parm.frcmod"
>
> 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.
> -Prashanth
>
>
>
>
>
>
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