Dear Robin & Jason,
Getting the test psf's in XPLOR format to pass chamber conversion was
indeed as simple as using -xpsf instead of -psf to pass the psf file.
Apologies for not noting that.
I could not pass my original system (with XPLOR format), however; I think
this may have to do with the 5+ character atom type names from CGenFF, but
haven't had the opportunity to test this yet.
I will try Sarah's solution when I get the chance - thanks, Sarah.
And while I'm apologising: I noticed the "-box bounding" syntax and the
"-box <x>,<y>,<z>[,<alpha>,<beta>,<gamma>]" syntax in parmed.py's help. I
was incorrectly assuming the "-box <x> <y> <z>" syntax that chamber uses.
Thanks,
Marc
On 6 August 2014 16:50, Robin Betz <robin.robinbetz.com> wrote:
> Chamber can now handle xplor style PSF files without doing this editing
> actually.
>
> I believe that the PSF file should be passed with the argument -xpsf
> instead to have it parse correctly (please verify this in the chamber help,
> I don't have access to a computer right now).
>
> This will probably fix the problems you saw with chamber failing to parse
> your PSF file.
>
> Hope this helps,
> Robin Betz
> On Aug 6, 2014 9:31 AM, "Sarah Witzke" <witzke.sdu.dk> wrote:
>
> > Dear Mark,
> >
> > Oh yeah - I should be more careful when reading the mails ;-) Sorry, I
> get
> > it now.
> > So, what I do for my systems to get the inpcrd and prmtop files:
> > 1) Do whatever the modifications in VMD
> > 2) Change the xplor-type psf file to a charmm type psf file with a tcl
> > script like this:
> >
> > xplor2charmm.psf:
> > ****
> > package require psfgen
> > topology charmm_all36_280813.top
> > resetpsf
> > readpsf xplor.psf
> > writepsf charmm charmm.psf
> > exit
> > ****
> >
> > I run the script with "vmd -dispdev text -e xplor2charmm.tcl >
> > xplor2charmm.out".
> >
> > 3) Insert a line of:
> > 0 0 !NUMLP NUMLPH
> >
> > If you have no cmap term, then this line should be inserted at the end of
> > the .psf file.
> > If you do have cmap terms, then this section should only be the second
> > last section.
> > For example here is the last few lines of a psf file with cmap terms
> > (!NCRTERM):
> >
> > ***
> > 1 0 !NGRP
> > 0 0 0
> >
> > 0 0 !NUMLP NUMLPH
> >
> >
> > 3 !NCRTERM: cross-terms
> > 56 216 218 224 216 218 224 229
> > 239 241 243 261 241 243 261 263
> > 261 263 265 271 263 265 271 276
> > ****
> >
> > 4) Run chamber (maybe ParmEd now)
> >
> > I always have to manually insert the section with !NUMLP when using psf
> > files from vmd in chamber.
> > Whether there is an easier way to do it, I don't know, but maybe this can
> > help you too?
> >
> > Best regards,
> > Sarah
> >
> >
> > Den 06/08/2014 kl. 14.01 skrev Marc van der Kamp <
> marcvanderkamp.gmail.com
> > >:
> >
> > > Dear Sarah,
> > >
> > > Thanks for your effort in checking this.
> > > To clarify:
> > > I meant that I have not been able to generate prmtop+inpcrd for my
> 'real'
> > > system of interest, for which I generated a psf with VMD's psfgen.
> > > I have used chamber several times before (successfully) using psf+crd
> > > generated by CHARMM. In my original post, I indicated that I was keen
> to
> > > use chamber for psfgen generated psf's, now AmberTools14 update.7
> > included
> > > "Better support for VMD psfgen files" (see
> > > http://ambermd.org/bugfixesat.html).
> > >
> > > I thought that this would mean that the X-PLOR style psf (with atom
> type
> > > names instead of numbers, as you pointed out) would be accepted, but
> > > perhaps I am wrong.
> > > As far as I know, psfgen can only write X-PLOR style psf's.
> > >
> > > Thanks,
> > > Marc
> > >
> > >
> > > On 6 August 2014 12:50, Sarah Witzke <witzke.sdu.dk> wrote:
> > >
> > >> Hi Marc,
> > >>
> > >> I am a bit confused - you said that you did not get a .inpcrd and a
> > >> .prmtop file yet, but further down in the mail you said that chamber
> did
> > >> successfully generate those files?
> > >> I have generated those files with chamber without problems - let me
> know
> > >> if you would like them.
> > >> Chamber does not like xplor type pst files due to the difference in
> the
> > >> 5th column of !NATOM section - notice the atom names vs. a number:
> > >>
> > >> non-xplor type:
> > >> 48 !NATOM
> > >> 1 A 1 MET N 72 -0.300000 14.0070
> > >>
> > >>
> > >> xplor type:
> > >> 48 !NATOM
> > >> 1 A 1 MET N NH3 -0.300000 14.0070
> > >>
> > >>
> > >> As for ParmEd I have not tried it - but I look forward to it :-)
> Thanks
> > >> Jason!
> > >>
> > >> Best regards,
> > >> Sarah
> > >>
> > >>
> > >> Den 06/08/2014 kl. 09.55 skrev Marc van der Kamp <
> > marcvanderkamp.gmail.com
> > >>> :
> > >>
> > >>> 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
> > >>>>>
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> AMBER mailing list
> > >>>>> AMBER.ambermd.org
> > >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>
> > >>>>
> > >>>>
> > >>> <test.tgz>_______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Aug 06 2014 - 09:30:04 PDT
