[AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)

From: Sarah Witzke <witzke.sdu.dk>
Date: Thu, 14 Aug 2014 16:31:16 +0000

Hi Jason,

I have downloaded the latest ParmEd from your github (just a couple of hours ago) and done "python setup.py build", "python setup.py install".
When I run ParmEd I give the full path to this executable to make sure I use this version.
I have a pdb and a psf file of a membrane containing POPC and ergosterol from the charmm-membrane-builder-gui. When I try to use chamber in ParmEd with this command:
*****
chamber -top top_all36_lipid.rtf -top top_all36_cgenff.rtf -param par_all36_lipid.prm -param par_all36_cgenff.prm -str toppar_all36_lipid_cholesterol.str -str toppar_water_ions.str -psf step5_assembly.psf -crd step5_assembly.pdb -box 72.5,72.5,82 -nocmap
*****
I get this error:
*****
Creating chamber topology file from PSF step5_assembly.psf, RTF files [top_all36_lipid.rtf, top_all36_cgenff.rtf], PAR files [par_all36_lipid.prm, par_all36_cgenff.prm], and STR files [toppar_all36_lipid_cholesterol.str, toppar_water_ions.str]. Coords from step5_assembly.pdb. NO CMAP. Box info [72.5, 72.5, 82.0, 90.0, 90.0, 90.0]. GB Radius set mbondi.
Traceback (most recent call last):
  File "/Users/witzke/ParmEd-1.1/parmed.py", line 161, in <module>
    parmed_commands.cmdloop()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py", line 142, in cmdloop
    stop = self.onecmd(line)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py", line 219, in onecmd
    return func(arg)
  File "<string>", line 1, in <lambda>
  File "/Users/witzke/ParmEd-1.1/ParmedTools/parmed_cmd.py", line 141, in _normaldo
    action.execute()
  File "/Users/witzke/ParmEd-1.1/ParmedTools/ParmedActions.py", line 3563, in execute
    parm.load_coordinates(coords)
  File "/Users/witzke/ParmEd-1.1/chemistry/amber/_amberparm.py", line 940, in load_coordinates
    for i, atom in enumerate(self.atom_list):
AttributeError: 'ChamberParm' object has no attribute 'atom_list'
*****

It seems similar to en error Marc had previously but I can't figure out what I should do differently. Do you have an idea?

Best regards,
Sarah


Start på videresendt besked:

Fra: Marc van der Kamp <marcvanderkamp.gmail.com<mailto:marcvanderkamp.gmail.com>>
Emne: Vedr.: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)
Dato: 11. aug. 2014 22.14.04 CEST
Til: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Svar til: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>

Hi Jason,
Did a git pull and ran setup.py to install (python setup.py install --user
--install-scripts ~/bin/)

Now upon starting parmed.py I immediately get an error:

Traceback (most recent call last):
 File "/Users/marcvanderkamp/Documents/work/ParmEd/parmed.py", line 11, in
<module>
   from ParmedTools.logos import Logo
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/__init__.py", line
12, in <module>
   import ParmedTools.ParmedActions as _PA
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/ParmedActions.py",
line 18, in <module>
   from ParmedTools.parmlist import ParmList, ChamberParm, AmoebaParm
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/parmlist.py", line
8, in <module>
   from chemistry.amber.readparm import AmoebaParm
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/readparm.py",
line 26, in <module>
   from chemistry.amber._amberparm import AmberParm, Rst7
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/_amberparm.py",
line 26, in <module>
   from chemistry.amber.topologyobjects import (Bond, Angle,
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/topologyobjects.py",
line 20, in <module>
   from compat24 import all, property
 File "/Users/marcvanderkamp/Documents/work/ParmEd/compat24.py", line 64,
in <module>
   if not hasattr(__builtins__.property, 'setter'):
AttributeError: 'dict' object has no attribute 'property'

Thanks,
Marc


On 11 August 2014 18:37, Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>> wrote:

On Mon, 2014-08-11 at 14:40 +0100, Marc van der Kamp wrote:
Dear Jason,
Thanks for your changes - I think the 'more flexible' PSF parser is a
good
idea.
The parameter file in the tarball was made manually, and I clearly made a
mistake. I didn't catch this myself before, as I've now been using the
-str
attribute (in chamber and parmed.py's chamber) to pass various additional
parameters. I had just used this single file for the test-case. So no
need
to add support for that, I would think.

OK, good :). One other note for ParmEd -- you can pass multiple -param
and -top flags (whereas with chamber, I think you need 1 param, 1 top,
and the rest have to be passed as stream files).

ParmEd is actually a bit stricter than chamber when reading stream files
-- it behaves more like CHARMM (I think), where it looks for commands to
read a topology section and a parameter section(look for the line "read
rtf card .app" and "read para card flex @app" in the
toppar_water_ions.str file bundled with the CHARMM force field, for
example). Since these command cards don't seem to be found by default
in parameter and topology files, I don't think you can pass those as
stream files to the chamber command in ParmEd.


I'm still having a problem with the test-case with ParmEd (on my
MacBook),
however.

I cloned & installed ParmEd fresh from github.
I changed the parameter file as you suggested (putting the NBFIX section
at
the end, just before END).
What I now get is:
chamber -top top_all36_prot_ksi.rtf -param
par_all36_prot_cgenff_ksi.prm
-psf dry.rs1_charmm.psf -crd dry.rs1.pdb
Creating chamber topology file from PSF dry.rs1_charmm.psf, RTF files
[top_all36_prot_ksi.rtf], and PAR files [par_all36_prot_cgenff_ksi.prm]
Coords from dry.rs1.pdb. Using CMAP. GB Radius set mbondi.
Traceback (most recent call last):
 File "/Users/marcvanderkamp/Documents/work/ParmEd/parmed.py", line 161,
in <module>
   parmed_commands.cmdloop()
 File

"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
line 142, in cmdloop
   stop = self.onecmd(line)
 File

"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cmd.py",
line 221, in onecmd
   return func(arg)
 File "<string>", line 1, in <lambda>
 File
"/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/parmed_cmd.py",
line 141, in _normaldo
   action.execute()
 File

"/Users/marcvanderkamp/Documents/work/ParmEd/ParmedTools/ParmedActions.py",
line 3563, in execute
   parm.load_coordinates(coords)
 File

"/Users/marcvanderkamp/Documents/work/ParmEd/chemistry/amber/_amberparm.py",
line 940, in load_coordinates
   for i, atom in enumerate(self.atom_list):
AttributeError: 'ChamberParm' object has no attribute 'atom_list'

I think I see why this is happening, and I've pushed a fix. What I'm
not exactly sure of is why I wasn't seeing this problem...

Can you see if this works now?

Thanks for helping me work out some of the kinks!
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 14 2014 - 10:00:02 PDT
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