On Aug 6, 2014, at 3:39 AM, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> Dear Jason (and others),
>
> I wasn't aware of this new functionality of ParmEd! Very impressed (and
> great that there is the NBFIX option as well!) - many thanks for your work,
> Jason!
>
> Now, I did encounter problems, and haven't been able to generate a
> prmtop+inpcrd of my system yet; for a tri-peptide test-system, I was only
> successful with chamber (not parmed.py) and a CHARMM-style psf (written by
> CHARMM). See details below.
>
> First, I believe the -cmap flag should not be used in parmed.py?
> When I try (after cloning and installing parmed.py as per your instructions
> - did this on my MacBook as away from work):
>> chamber -cmap -top top_all36_prot_ksi.rtf -param
> par_all36_prot_cgenff_ksi.prm -psf ionized.psf -crd ionized.pdb
> Action chamber failed
> UnhandledArgumentWarning: -cmap
>
> Without the -cmap flag but with specifying a -box, I get:
> chamber -top top_all36_prot_ksi.rtf -param par_all36_prot_cgenff_ksi.prm
> -psf ionized.psf -crd ionized.pdb -box 72.18 83.12 69.77
> Action chamber failed
> InputError: Box must be 3 lengths or 3 lengths and 3 angles!
Ah, apologies here. One of the choices I made was that any PSF file that specified CMAP terms would automatically use CMAPs. This could be explicitly disabled using "-nocmap", but the "-cmap" flag is no longer necessary. CMAPs are not nearly as new now as they were when chamber was originally written, and omitting them in modern force fields is just wrong.
Also, ParmEd is much like cpptraj with respect to how it handles arguments. It always tries to pull one argument off the stack or two in the case of keyword arguments. So you need to change the box argument to "-box <x>,<y>,<z>[,<alpha>,<beta>,<gamma>]" (with no spaces). You can use "?chamber" or "help chamber" to get a full listing of how to use the command.
> (and adding 90.0 90.0 90.0 for angles doesn't help)
>
> How should I specify the 'boundingbox' option?
"-box bounding" (this is also put in the help text, but was incorrectly described in my last email).
I will try with your files shortly.
Thanks!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 06 2014 - 09:00:03 PDT
