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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 06 2014 - 09:00:04 PDT
