I imagine that Jason will have the final word on this once he sees it,
but my guess is that the RTF/PRM files are not as close to the usual
CHARMM force field as was used in designing/debugging parmed.
Since the CHAMBER command (and program) was specifically designed to
account for those force field features not in common with the AMBER
force field, it is not finding something it is looking for. If I recall
correctly (that's a big if), OPLS/AA has more in common with the
functional form for AMBER than for CHARMM, so maybe exporting an frcmod
is the way to go here? If there is an old OPLA lib file lying around,
you might be able to use that and then re-define the atoms types. Also,
you may have to go back and redo LJ cross terms "by hand", unless ParmEd
is clever enough to do geometric mixing of A/B terms at this point.
Regards,
Brian
On 06/22/2015 10:54 AM, Karl Debiec wrote:
> Hi all,
>
> I am interested in testing the recently published OPLS-AA/M force field (
> http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00356) in AMBER. The force
> field is available in CHARMM format (http://zarbi.chem.yale.edu/oplsaam.html),
> and I am hoping to build my system (an Ace-Ala-Ala-Ala-Nme tetrapeptide)
> using NAMD/VMD's psfgen and convert the resulting topology to AMBER format
> using parmed's chamber command.
>
> This pipeline works well for CHARMM36, but I'm having trouble with
> OPLS-AA/M, and before investing to much time I'd like to check if 1) anyone
> else has worked through this, and 2) trying to run OPLS-AA/M in AMBER makes
> sense at all.
>
> My first attempt using the above linked topology and parameters sets with
> the psf and pdb files output from psfgen yields the following traceback:
>
> Reading input from STDIN...
>> chamber -top ../toppar/top_opls_aam.inp -param ../toppar/par_opls_aam.inp
> -psf ALAALAALA.psf -crd ALAALAALA.pdb -box bounding -nocmap
> Creating chamber topology file from PSF ALAALAALA.psf, RTF files
> [../toppar/top_opls_aam.inp], and PAR files [../toppar/par_opls_aam.inp]
> Coords from ALAALAALA.pdb. NO CMAP. Defining a bounding box. GB Radius set
> mbondi.
> Traceback (most recent call last):
> File
> "/share/home/ktd3/software/amber/14_intel-11.1_openmpi-1.8.3_devel/bin/parmed",
> line 6, in <module>
> clapp()
> File
> "/share/home/ktd3/software/amber/14_intel-11.1_openmpi-1.8.3_devel/lib/python2.7/site-packages/parmed/scripts.py",
> line 193, in clapp
> parmed_commands.cmdloop()
> File "/share/apps/anaconda/2.1.0/lib/python2.7/cmd.py", line 142, in
> cmdloop
> stop = self.onecmd(line)
> File "/share/apps/anaconda/2.1.0/lib/python2.7/cmd.py", line 221, in
> onecmd
> return func(arg)
> File "<string>", line 1, in <lambda>
> File
> "/share/home/ktd3/software/amber/14_intel-11.1_openmpi-1.8.3_devel/lib/python2.7/site-packages/parmed/tools/parmed_cmd.py",
> line 153, in _normaldo
> action.execute()
> File
> "/share/home/ktd3/software/amber/14_intel-11.1_openmpi-1.8.3_devel/lib/python2.7/site-packages/parmed/tools/actions.py",
> line 3771, in execute
> parmset.read_parameter_file(pfile)
> File
> "/share/home/ktd3/software/amber/14_intel-11.1_openmpi-1.8.3_devel/lib/python2.7/site-packages/parmed/charmm/parameters.py",
> line 517, in read_parameter_file
> key)
> RuntimeError: Atom type SOD not present in AtomType list
>
> My system does not contain counterions, so I tried deleting the SOD and CLA
> lines from the parameter file. Chamber now fails more smoothly, but still
> cannot build the system:
>
> Reading input from STDIN...
>> chamber -top ../toppar/top_opls_aam.inp -param ../toppar/par_opls_aam.inp
> -psf ALAALAALA.psf -crd ALAALAALA.pdb -box bounding -nocmap
> Creating chamber topology file from PSF ALAALAALA.psf, RTF files
> [../toppar/top_opls_aam.inp], and PAR files [../toppar/par_opls_aam.inp]
> Coords from ALAALAALA.pdb. NO CMAP. Defining a bounding box. GB Radius set
> mbondi.
> Action chamber failed
> ChamberError: Problem assigning parameters to PSF: Missing bond
> type for <Bond <Atom CAY [0]; In ALA 0>--<Atom HY1 [1]; In ALA 0>;
> type=None>
>
> The bond between these two atoms (types C135 and H140) is present in the
> parameter file. Has anyone else worked through these issues?
>
> Thanks,
> Karl Debiec
>
--
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Mon Jun 22 2015 - 14:00:02 PDT
