VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Sat Apr 30 2011 - 10:16:16 CDT

Ah, I see. Thanks Axel, I will revert to the psfgen method then.

E

On Fri, Apr 29, 2011 at 4:11 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Apr 29, 2011 at 3:30 PM, Edward Lyman <edward.lyman_at_gmail.com>
> wrote:
> > Thanks for the reply. Now I have used vmd 1.9 to delete a single
> cholesterol
> > by
> >
> > (1) read in psf and pdb for the full system
> > (2) define an atom selection that excludes the problematic cholesterol:
> >> set write_sel [atomselect top "not same fragment as index foo"]
> > (3) renumber residues
> >> $write_sel set resid [$write_sel get residue]
> > (4) write psf/pdb
> > > $write_sel writepsf new.psf
> > > $write_sel writepdb new.pdb
> >
> > This writes a psf that looks ok through the bonds section, but the
> angles,
> > dihedrals, impropers have problems. There are the same number of angles
> in
> > the new as in the original psf. (Theres hould be fewer because there is
> one
> > less chol) And, the angles include triplets like "1 2 2 " in the first 50
> or
> > so lines, then the angle lines are all "1 1 1 1 1 1 1 1 ". same for
> > dihedrals, etc.
> >
> > So, am I missing an autogenerate statement? It seems possible that
> > autogenerate may not get the angles, dihedrals etc correct...is that a
> real
> > concern?
>
> ed,
>
> you are touching a real problem. i didn't think about this earlier.
> the bond information is attached to the atom information and thus
> will be adjusted accordingly. however, this is not true for angles and
> dihedrals or impropers. that information is stored separately, and
> then not subjected to any selection operations.
>
> i guess, that may be the reason for people to keep using psfgen
> for these tasks. while not a VMD intrinsic, you could loading the
> psf/pdb combo with the atoms deleted and then use the "guess" commands
> of the topotools plugin to redo the angle, dihedral and improper
> definitions.
>
>
> http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-guess-angle-dihedral-s
>
> however, there is one caveat. this will generate this information from
> the bond topology alone, and thus may not always be the same
> as what psfgen will generate, particularly for impropers. you might
> need to run some tests on this. i did some successful tests on
> simple peptides, but never for a large protein.
>
> sorry for overlooking the angles stuff. that was my bad.
>
> axel.
>
> >
> > Thanks,
> > Ed
> >
> >
> > On Fri, Apr 29, 2011 at 9:40 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Fri, Apr 29, 2011 at 9:00 AM, Edward Lyman <edward.lyman_at_gmail.com>
> >> wrote:
> >> > Thanks for the work around, it's very much appreciated. But, it occurs
> >> > to me
> >> > now...why can't I simply use $sel writepsf blah.psf and $sel writepdb
> >> > blah.pdb from the vmd console to write out a psf and a pdb for
> >> > selections
> >> > which delete the unwanted molecules? ie, why bother with psfgen at all
> >> > when
> >> > you already have in hand a psf that contains all the correct force
> field
> >> > terms, etc, and you just want to delete a few molecules?
> >>
> >> you can do this. the functionality to store and write out the complete
> >> topology
> >> information from and to .psf files has not been around that long and
> >> before that
> >> using psfgen was the only option. not everybody is aware of this new
> >> functionality
> >> in VMD and various plugins and scripts are only slowly being migrated to
> >> make
> >> use of these new features (why break something that works?).
> >>
> >> cheers,
> >> axel.
> >>
> >> >
> >> > Thx,
> >> > Ed
> >> >
> >> >
> >> >
> >> >
> >> > On Tue, Apr 26, 2011 at 3:21 PM, Jim Phillips <jim_at_ks.uiuc.edu>
> wrote:
> >> >>
> >> >> If you can't get CHARMM-GUI to write a non-EXT, non-CHEQ format PSF
> (I
> >> >> don't think you need either of those options) then try reading the
> file
> >> >> into
> >> >> VMD, writing it out again, and using that file with psfgen.
> >> >>
> >> >> If you use the psfgen binary from NAMD 2.8b1 you can probably read
> the
> >> >> file with "readmol psf 50_50_10nm.xplor.psf" since that uses the VMD
> >> >> plugins
> >> >> (I don't think VMD's psfgen module has plugins enabled yet).
> >> >>
> >> >> -Jim
> >> >>
> >> >>
> >> >> On Tue, 26 Apr 2011, Edward Lyman wrote:
> >> >>
> >> >>> attached is the psf.
> >> >>>
> >> >>> Any suggestions for a workaround? I want to delete a couple lipid
> >> >>> molecules
> >> >>> as described in the psfgen docs...if there is some othe way to
> >> >>> accomplish
> >> >>> this, I am all ears.
> >> >>>
> >> >>> E
> >> >>>
> >> >>>
> >> >>> On Tue, Apr 26, 2011 at 11:53 AM, John Stone <johns_at_ks.uiuc.edu>
> >> >>> wrote:
> >> >>>
> >> >>>> Hi,
> >> >>>> It seems that psfgen doesn't like the X-PLOR format PSF file
> you've
> >> >>>> got,
> >> >>>> although the VMD PSF plugin seems to read it without trouble.
> >> >>>>
> >> >>>> Can you send me a gzipped copy of the PSF file that is causing you
> >> >>>> trouble?
> >> >>>>
> >> >>>> This is most likely a limitation of the PSF reader currently in
> >> >>>> psfgen,
> >> >>>> and is something we are looking at improving.
> >> >>>>
> >> >>>> Cheers,
> >> >>>> John Stone
> >> >>>> vmd_at_ks.uiuc.edu
> >> >>>>
> >> >>>> On Fri, Apr 22, 2011 at 11:03:30AM -0400, Edward Lyman wrote:
> >> >>>>>
> >> >>>>> Hi all,
> >> >>>>>
> >> >>>>> I am trying to use psfgen to delete a couple of lipids and write
> a
> >> >>>>> new
> >> >>>>> psf/pdb pair. The toplogy files read in fine, but when I read
> teh
> >> >>>>> psf,
> >> >>>>
> >> >>>> I
> >> >>>>>
> >> >>>>> get:
> >> >>>>>
> >> >>>>> reading structure from psf file 50_50_10nm.xplor.psf
> >> >>>>> Error processing bonds
> >> >>>>>
> >> >>>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> >> >>>>> psfplugin) Detected a Charmm31 PSF file
> >> >>>>> psfplugin) Detected a Charmm31 PSF EXTEnded file
> >> >>>>> Info) Using plugin psf for structure file 50_50_10nm.xplor.psf
> >> >>>>> psfplugin) no cross-terms defined in PSF file.
> >> >>>>> Info) Analyzing structure ...
> >> >>>>>
> >> >>>>> I am running vmd 1.9, psfgen 1.5. The psf file is an xplor psf
> >> >>>>> (runs
> >> >>>>
> >> >>>> in
> >> >>>>>
> >> >>>>> namd) that was written by the charmm gui. The psf/pdb pair work
> >> >>>>> just
> >> >>>>
> >> >>>> fine
> >> >>>>>
> >> >>>>> for reading into vmd.
> >> >>>>>
> >> >>>>> Any help is appreciated.
> >> >>>>> Ed
> >> >>>>
> >> >>>> --
> >> >>>> NIH Resource for Macromolecular Modeling and Bioinformatics
> >> >>>> Beckman Institute for Advanced Science and Technology
> >> >>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> >>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >> >>>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> >> >>>>
> >> >>>
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>