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
--
Karl Debiec
Graduate Student, Molecular Biophysics & Structural Biology
University of Pittsburgh
Chong Group, Department of Chemistry
Gronenborn Group, Department of Structural Biology
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Received on Mon Jun 22 2015 - 09:00:03 PDT
