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
>>
>>
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>>
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Received on Wed Aug 06 2014 - 09:00:02 PDT
