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
>>>
>>
>>
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Received on Wed Aug 06 2014 - 05:00:02 PDT
