Hi Jason,
Thank you for your reply. I assume the executable to be parmed that will
job similar job as that of chamber. As per your suggestion,
I have installed AmberTools18 to do this conversion. I am using the
following command
$AMBERHOME/bin/parmed -top top_all36_prot.rtf -param par_all36m_prot.prm
-cmap -xpsf Willbold_IRF_1-42_6X2.psf -crd -p prot.prmtop -inpcrd
prot.inpcrd
However, I am receiving the following error.
Traceback (most recent call last):
File "/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/bin/parmed", line
6, in <module>
from pkg_resources import load_entry_point
File
"/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 3126, in <module>
._call_aside
File
"/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 3110, in _call_aside
f(*args, **kwargs)
File
"/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 3139, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File
"/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 581, in _build_master
ws.require(__requires__)
File
"/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 898, in require
needed = self.resolve(parse_requirements(requirements))
File
"/home/prabir/SOFTWARE/AMBER/AMBER_TOOLS/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py",
line 784, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ParmEd==3.0.0+57.g74a84d30'
distribution was not found and is required by the application
Can you please tell me what I am doing wrong and how to fix this?
Thanks,
Prabir
On Thu, Feb 7, 2019 at 10:29 AM Jason Swails <jason.swails.gmail.com> wrote:
> The chamber program has been replaced by the "chamber" action inside
> ParmEd, which will hopefully not suffer from this problem.
>
> I suggest updating to the latest version of AmberTools and use parmed from
> there. Inside the parmed interpreter, you can type "help chamber" for
> instructions on use (it is used in much the same way as chamber from Amber
> 14).
>
> As a note, chamber is no longer built, as its functionality is incorporated
> into ParmEd.
>
> On Tue, Feb 5, 2019 at 4:47 PM Prabir Khatua <prabir07chem.gmail.com>
> wrote:
>
> >
> > I have one more query. CHAMBER is not allowing me to run this command
> > without mentioning cmap option. Thus, tt seems to be mandatory. I am not
> > sure whether I should turn on cmap or not for charmm36. Please suggest me
> > what to do. Any suggestion would be appreciated.
> >
>
> Yes, use CMAPs. With ParmEd in AmberTools 18, this is determined
> automatically for you (if the system specifies CMAPs in the PSF file,
> they're added automatically).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
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Received on Tue Feb 12 2019 - 11:00:04 PST
