Dear Jason (and others),
I wasn't aware of this new functionality of ParmEd! Very impressed (and
great that there is the NBFIX option as well!) - many thanks for your work,
Jason!
Now, I did encounter problems, and haven't been able to generate a
prmtop+inpcrd of my system yet; for a tri-peptide test-system, I was only
successful with chamber (not parmed.py) and a CHARMM-style psf (written by
CHARMM). See details below.
First, I believe the -cmap flag should not be used in parmed.py?
When I try (after cloning and installing parmed.py as per your instructions
- did this on my MacBook as away from work):
> chamber -cmap -top top_all36_prot_ksi.rtf -param
par_all36_prot_cgenff_ksi.prm -psf ionized.psf -crd ionized.pdb
Action chamber failed
UnhandledArgumentWarning: -cmap
Without the -cmap flag but with specifying a -box, I get:
chamber -top top_all36_prot_ksi.rtf -param par_all36_prot_cgenff_ksi.prm
-psf ionized.psf -crd ionized.pdb -box 72.18 83.12 69.77
Action chamber failed
InputError: Box must be 3 lengths or 3 lengths and 3 angles!
(and adding 90.0 90.0 90.0 for angles doesn't help)
How should I specify the 'boundingbox' option?
Then, I proceeded to test parmed.py's chamber command and the
$AMBERTOOLS/bin/chamber with a simple tri-peptide system. I generated 3
different psf files:
- test.psf: CHARMM-style psf with charmm (v36)
- test_xplor: X-PLOR-style psf as written by charmm (v36)
- dry.test.psf: X-PLOR style psf as written by VMD's psfgen
For the CHARMM-generated psf's, I used the corresponding test.crd file
written by charmm, for the psfgen-generated psf, I used the corresponding
dry.test.pdb file written by VMD/psfgen. For the protein parameters and
topology, I used the most recent files available on MacKerell's website (
from toppar_c36_dec13.tgz
<
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_dec13.tgz>
).
Below are first the initial ATOM lines of the psf, and then the 'results'
from chamber and parmed.py's chamber command.
CHARMM-style psf:
48 !NATOM
1 A 1 MET N 72 -0.300000 14.0070 0
0.00000 -0.301140E-02
2 A 1 MET HT1 32 0.330000 1.00800 0
0.00000 -0.301140E-02
3 A 1 MET HT2 32 0.330000 1.00800 0
0.00000 -0.301140E-02
chamber:
chamber -cmap -top top_all36_prot.rtf -param par_all36_prot.prm -psf
test.psf -crd test.crd
(prmtop + inpcrd succesfully generated)
parmed.py:
> chamber -top top_all36_prot.rtf -param par_all36_prot.prm -psf test.psf
-crd test.crd
Creating chamber topology file from PSF test.psf, RTF files
[top_all36_prot.rtf], and PAR files [par_all36_prot.prm] Coords from
test.crd. Using CMAP. 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 3563, in execute
parm.load_coordinates(coords)
File
"/Users/marcvanderkamp/Library/Python/2.7/lib/python/site-packages/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'
X-PLOR style psf written by CHARMM:
48 !NATOM
1 A 1 MET N NH3 -0.300000 14.0070 0
0.00000 -0.301140E-02
2 A 1 MET HT1 HC 0.330000 1.00800 0
0.00000 -0.301140E-02
3 A 1 MET HT2 HC 0.330000 1.00800 0
0.00000 -0.301140E-02
chamber:
chamber -cmap -top top_all36_prot.rtf -param par_all36_prot.prm -psf
test.psf -crd test.crd
At line 2349 of file psfprm.F90
Fortran runtime error: Bad value during integer read
parmed.py:
> chamber -top top_all36_prot.rtf -param par_all36_prot.prm -psf
test_xplor.psf -crd test.crd
Creating chamber topology file from PSF test_xplor.psf, RTF files
[top_all36_prot.rtf], and PAR files [par_all36_prot.prm] Coords from
test.crd. Using CMAP. 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 3563, in execute
parm.load_coordinates(coords)
File
"/Users/marcvanderkamp/Library/Python/2.7/lib/python/site-packages/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'
X-PLOR-style psf written by VMD's psfgen:
48 !NATOM
1 PROA 1 MET N NH3 -0.300000 14.0070 0
2 PROA 1 MET HT1 HC 0.330000 1.0080 0
3 PROA 1 MET HT2 HC 0.330000 1.0080 0
chamber:
chamber -cmap -top top_all36_prot.rtf -param par_all36_prot.prm -psf
dry.test.psf -crd dry.test.pdb
At line 2349 of file psfprm.F90
Fortran runtime error: Bad value during integer read
parmed.py:
> chamber -top top_all36_prot.rtf -param par_all36_prot.prm -psf
dry.test.psf -crd dry.test.pdb
Creating chamber topology file from PSF dry.test.psf, RTF files
[top_all36_prot.rtf], and PAR files [par_all36_prot.prm] Coords from
dry.test.pdb. Using CMAP. GB Radius set mbondi.
Action chamber failed
ChamberError: Problem reading CHARMM PSF
The parmed.py errors for the psf's written by CHARMM may be due to my
installation?
The parmed.py error for the psf written by psfgen appear to be a formatting
issue?
Any hints/help greatly appreciated, as always.
--Marc
On 5 August 2014 20:30, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Aug 5, 2014, at 12:27 PM, Marc van der Kamp <marcvanderkamp.gmail.com>
> wrote:
>
> > Hello,
> >
> > Encouraged by the recent update of chamber related to better support for
> > VMD psfgen generated psf files, I decided to try it out (after updating
> > AmberTools14 with updates 1-7 and recompiling).
> >
> > Unfortunately, when I ran:
> > $AMBERHOME/bin/chamber -cmap -top top_all36_prot_lig.rtf -param
> > par_all36_prot_cgenff_lig.prm -psf ionized.psf -crd ionized.crd -p
> > 1ohp_rs1_charmm.prmtop -inpcrd 1ohp_rs1_charmm.inpcrd -box 72.180 83.115
> > 69.771
> >
> > (or variations on this, e.g. with -str to add the additional
> > parameters/topogies)
> > I get the following error:
> >
> > At line 2349 of file psfprm.F90
> > Fortran runtime error: Bad value during integer read
> >
> > I've run out of time to do more testing today (and no time tomorrow), so
> I
> > would like to check if anyone has seen this or has an idea what it may be
> > caused by.
> >
> > lines 2341-2349 in psfprm.F90:
> >
> > read(psf_unit,fmt01) ii, & ! 1
> > lsegid, & ! AAL
> > iresid(i), & ! 1
> > lresat(i), & ! ASN
> > atom_label(i), & ! N
> > iac(i), & ! 54
> > cg(i), & ! -0.47000
> > amass(i), & ! 14.0070
> > imove(i) ! 0
> >
> >
> > Any insight welcome; many thanks in advance!
>
> I think we would actually need the PSF file in order to determine how the
> assumption of the line layout breaks the assumptions made in chamber.
>
> There is an alternative to chamber that you can try, however. See
> http://github.com/swails/ParmEd for an updated version of the ParmEd
> program that is bundled with AmberTools. ParmEd has a new action "chamber"
> that will create chamber-style topology files from PSF and CHARMM
> coordinate, restart, or PDB files with a syntax that is almost identical to
> the chamber program itself. I've found that it is quite a bit more
> flexible in terms of what PSF files it will successfully parse, and it has
> a number of additional advantages as well. Particularly:
>
> 1. If you use VMD to create a PSF and PDB file, it will pull the box
> information from the PDB file so you don't have to specify it in the
> CHAMBER command.
> 2. It accepts a new keyword "boundingbox" that will assign an orthorhombic
> box that encloses all atom centers
> 3. It supports and implements NBFIX modifications defined in CHARMM
> parameter or stream files (ion parameters in CHARMM36 all have NBFIXes, to
> my knowledge)
> 4. The topology files generated by ParmEd are notably smaller because it
> compresses degenerate parameter types when possible.
>
> Obviously #3 is the most important improvement, since it's the difference
> between "correct" and "incorrect" implementations of the CHARMM force field
> in the eyes of many reviewers, whereas #1, 2, and 4 are more convenience
> options than anything else (#4 can have performance implications,
> particularly with pmemd.cuda when NBFIX mods are present. Fewer atom types
> means that the LJ coefficient matrices are more likely to fit inside the
> device cache and thereby avoid costly latencies associated with what is
> effectively a cache miss -- I'm not sure when or if this becomes
> significant or noticeable).
>
> To use it, download and install ParmEd using a command like:
>
> python setup.py build
> python setup.py install [--user] [--install-scripts <directory>]
>
> Where --install-scripts allows you to specify where parmed.py and
> xparmed.py are installed, and the --user command will install the Python
> modules in your home directory (but still in a place where they will be
> found by default by the Python interpreter). Then you can use parmed.py
> something like:
>
> $ parmed.py
> > chamber -cmap -top top_all36_prot_lig.rtf \
> -param par_all36_prot_cgenff_lig.prm \
> -psf ionized.psf -crd ionized.crd \
> -box 72.180 83.115 69.771
> > outparm 1ohp_rs1_charmm.prmtop 1ohp_rs1_charmm.inpcrd
>
> The only major differences in usage here is that you can supply multiple
> parameter or topology files, using a separate "-param <parameter_file>",
> "-top <rtf_file>", or "-str <stream_file>" argument. You can also add the
> keyword "usechamber" to have ParmEd invoke chamber to create the prmtop
> file (although it won't work if chamber can't parse the PSF file). This
> was added to help people validate ParmEd's converter.
>
>
> Another thing ParmEd can do is write PSF files. So if ParmEd can read the
> PSF file, you can write a quick script that will read the PSF file in and
> then print a new one that chamber can recognize. A quick python script
> like:
>
> from chemistry.charmm.psf import CharmmPsfFile
>
> psf = CharmmPsfFile('ionized.psf')
> psf.write_psf('fixed.psf')
>
>
> will write a PSF file that chamber can read.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Aug 06 2014 - 01:00:02 PDT
