I'm attaching the tri-peptide test psf's, crd and pdb as described in my
previous message here (in test.tgz), in case anyone wants to test this.
Thanks,
Marc
On 6 August 2014 08:39, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> 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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>>
>
>
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Received on Wed Aug 06 2014 - 01:00:03 PDT
