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

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Thu, 7 Aug 2014 16:58:12 +0100

Hi Jason,

Perhaps the LJ parameters are the problem, but not the only one... ;)
FYI, chamber (now working, with the instructions from Sarah earlier in this
thread) reports:
   --- Found all atom types in topology file

WARNING: No NONBONDED parameter section in this stream file:
| /users/chmwvdk/toppar/c36_dec13/top_all36_cgenff.rtf
WARNING: No NONBONDED parameter section in this stream file:
| ../RS1.str.txt

   --- Found all nonbond parameters

I tried to make a 'simple' CGenFF test-case for parmed.py based on my
system - just the ligand (with CGenFF atom types) and some water molecules.
But now I consistently get the following error from parmed.py
Action chamber failed
ChamberError: Problem reading CHARMM PSF

This is the case with a XPLOR-style and a CHARMM-style psf (with the latter
including the " 0 0 !NUMLP NUMLPH" line that Sarah indicated
should be added for chamber compatibility).

Attached is a tarball with this test system, with:
dry.rs1.psf - the XPLOR psf
dry.rs1_charmm.psf - the CHARMM psf
dry.rs1.pdb - the coordinates

The top and par files are also included, and I ran this by using the
following command in parmed.py:

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.
Action chamber failed
ChamberError: Problem reading CHARMM PSF

Hope this helps!

Thanks,
Marc
PS Thanks to Sarah and Michael, I got my original system converted using
chamber and some manual changes, incl. the NBFIX applied through ParmEd.


On 7 August 2014 16:27, Jason Swails <jason.swails.gmail.com> wrote:

> On Thu, Aug 7, 2014 at 7:53 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com>
> wrote:
>
> > Hi Jason,
> > I don't know yet if ParmEd handles the CGenFF atom types, as I am still
> > stuck with the following error (I get similar errors for the test
> systems,
> > CHARMM-style and XPLOR-style psf's alike - see previous email for
> details):
> >
> >
> > > chamber -top top_all36_prot_ksi.rtf -param
> par_all36_prot_cgenff_ksi.prm
> > -psf ionized.psf -crd ionized.pdb -box bounding
> > Creating chamber topology file from PSF ionized.psf, RTF files
> > [top_all36_prot_ksi.rtf], and PAR files [par_all36_prot_cgenff_ksi.prm]
> > Coords from ionized.pdb. Using CMAP. Defining a bounding box. GB Radius
> set
> > mbondi.
> > Traceback (most recent call last):
> > File "/Users/marcvanderkamp/bin/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/Library/Python/2.7/lib/python/site-packages/ParmedTools/parmed_cmd.py",
> > line 141, in _normaldo
> > action.execute()
> > File
> >
> >
> "/Users/marcvanderkamp/Library/Python/2.7/lib/python/site-packages/ParmedTools/ParmedActions.py",
> > line 3561, in execute
> > parm = ConvertFromPSF(psf, frcfield).view(ChamberParm)
> > File
> >
> >
> "/Users/marcvanderkamp/Library/Python/2.7/lib/python/site-packages/chemistry/amber/_chamberparm.py",
> > line 692, in ConvertFromPSF
> > rij = lj_radii[i] + lj_radii[j]
> > TypeError: unsupported operand type(s) for +: 'float' and 'NoneType'
> >
>
> ​Ah, it looks like one of the LJ parameters was not set. If these files
> are included in the tarball you attached earlier, I will try to reproduce
> this problem and make a fix. It would be great getting ParmEd working for
> any CHARMM system people have.
> ​
>
> > ​​
> > As mentioned before, this is probably a consequence of how parmed.py is
> > ​​
> > installed and my shell environment (?) but any hints on how to solve this
> > ​​
> > would be greatly appreciated.
> > ​​
> >
> > ​​
> > Thanks,
> > ​​
> > Marc
>
>
> ​Thanks!
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Thu Aug 07 2014 - 09:30:02 PDT
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