VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Jun 15 2010 - 11:57:12 CDT

Axel, when I try to set the last selection to "set sel3 [atomselect $mol2 ion]" I get no ions in the psf file still! I thought of using the CL as it is a .gro file. I should have looked at VMD terminal for error messages but I forgot.

The question now is how to include the ions in the .psf file. I can still do that manually.

Thanks
Rabab Toubar

--- On Tue, 6/15/10, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Subject: Re: topotools
> To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> Date: Tuesday, June 15, 2010, 12:31 PM
> On Tue, 2010-06-15 at 09:22 -0700,
> Rabab Toubar wrote:
> > Hi Axel,
> > I have another problem now, using your suggested tcl
> script
> > #load .gro and .psf file into vmd
> > set mol1 [mol new pr.psf waitfor all]
> > set mol2 [mol new pr.gro waitfor all]
> >
> > set sel1 [atomselect $mol1 all]
> > set sel2 [atomselect $mol2 water]
> > set sel3 [atomselect $mol2 CL]
>
> the last selection is wrong.
>
>
> > # Recalculate bonds
> > mol2 bondsrecalc $mol2
> > topo retypebonds
> >
> > # merge selections into new molecule.
> > package require topotools
> > ::TopoTools::selections2mol "$sel1 $sel2 $sel3"
> >
> > # write out new molecule
> > animate write psf axel_new.psf
> >
> > this gives me the correct number of atoms in the
> system, but with no charges for the protein, but if I use
> ::TopoTools::selections2mol "$sel1 $sel2" the charges are
> correct, but obviously I have no chloride ions
> >
> > I tried to look into the topotools plugin and
> everything in the script looks OK for me
>
> of course the scripts are ok, but it you feed them
> garbage,
> they'll also produce garbage. if $sel3 does not contain a
> reference to a proper atom selection then they'll fail.
>
> you have to very closely watch the output of the script.
> there have to be error messages and for as long as you
> are ignoring them, there is nothing that the topotools
> script can do about it.
>
> PEBCAC!
>
> axel.
>
> > Thanks
> > Rabab Toubar
> >
> >
> >
> > --- On Tue, 6/15/10, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >
> > > From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > Subject: Re: vmd-l: top2psf.tcl
> > > To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > > Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> > > Date: Tuesday, June 15, 2010, 11:31 AM
> > > On Tue, Jun 15, 2010 at 11:14 AM,
> > > Rabab Toubar <rtoubar_at_yahoo.com>
> > > wrote:
> > > > Using the tcl script you sent me, I am
> getting 11628
> > > atoms, bonds present, & the protein is
> charged but not
> > > the water (I believe I'm getting the protein
> charges from
> > > the top file)
> > > > 11628 !NATOM
> > > >       1 MAIN
> 1    ASP  N    NL 
>    0.129000
> > >       14.0067 
>          0
> > > >       2 MAIN
> 1    ASP  H1   H   
>   0.248000
> > >        1.0080   
>        0
> > > >
> > > > modifying the .tcl script so as to add ions
> that are
> > > found in my simulations, I am losing bonds and
> charges but
> > > having the correct number of atoms 11632..So I am
> just
> > > curious what is going on.
> > > >
> > > > #load .gro and .psf file into vmd
> > > > set mol1 [mol new myfile.psf waitfor all]
> > > > set mol2 [mol new myfile.gro waitfor all]
> > > > set sel1 [atomselect $mol1 all]
> > > > set sel2 [atomselect $mol2 water]
> > > > set sel3 [atomselect $mol3 ion]
> > >
> > > this one cannot work. there is no $mol3.
> > >
> > > set sel3 [atomselect $mol2 ion]
> > >
> > > to reset the charges and/or other properties,
> > > all you have to do is to build the proper
> selections
> > > and then set the values before combining them.
> > > for example.
> > >
> > > set sel4 [atomselect $mol2 "type OW"]
> > > $sel4 set charge -0.84
> > > set sel5 [atomselect $mol2 "type HW"]
> > > $sel5 set charge 0.42
> > >
> > > and so on.
> > >
> > > cheers,
> > >    axel.
> > >
> > > > # merge selections into new molecule.
> > > > package require topotools
> > > > ::TopoTools::selections2mol "$sel1 $sel2
> $sel3"
> > > >
> > > > # write out new molecule
> > > > animate write psf combined.psf
> > > >
> > > > 11632 !NATOM
> > > >       1 
>     1    ASP  N   
> N   
> > >  0.000000   
>    14.0070       
>    0
> > > >       2 
>     1    ASP 
> H1   H1   
> > > 0.000000        1.0080 
>          0
> > > >
> > > > Thanks, bondsrecalc made the bonds appear in
> the psf,
> > > and sorry for the email format & the cc; it
> was
> > > unintended.
> > > >
> > > > Rabab
> > > >
> > > > --- On Tue, 6/15/10, Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > wrote:
> > > >
> > > > From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > > Subject: Re: vmd-l: top2psf.tcl
> > > > To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > > > Date: Tuesday, June 15, 2010, 10:48 AM
> > > >
> > > > On Tue, Jun 15, 2010 at 10:38 AM, Rabab
> Toubar <rtoubar_at_yahoo.com>
> > > wrote:
> > > >>
> > > >> Hi Axel,
> > > >>
> > > >> using "animate" I get the correct number
> of atoms,
> > > but all the charges are set to zeros, and I have
> no bonds
> > > >> 11632 !NATOM
> > > >>        1 
>     1    ASP  N   
> > > N      0.000000   
>    14.0070         
>
> > > 0
> > > >>        2 
>     1    ASP  H1 
> > > H1     0.000000   
>     1.0080         
> > > 0
> > > >>        3 
>     1    ASP  H2 
> > > H2     0.000000   
>     1.0080         
> > > 0
> > > >
> > > > well, you cannot have what is not there. a
> .gro file
> > > has
> > > > not information about atom charges, so there
> are not
> > > > in the resulting .psf file.
> > > >
> > > >> 0 !NBOND: bonds
> > > >>        0 !NTHETA:
> angles
> > > >>       0 !NPHI:
> dihedrals
> > > >>        0 !NIMPHI:
> impropers
> > > >>       0 !NDON:
> donors
> > > >>       0 !NACC:
> acceptors
> > > >>
> > > >> the second "untested" method worked well
> but not
> > > including the ions. It had the charges for the
> atoms and
> > > everything. So I tried to modify the tcl script
> by adding a
> > > 3rd selection "set sel3 [atomselect $mol3 ion]"
> when I got
> > > zero charges and zero bonds as the 1st case. I
> donot
> > > understand why; any guesses?
> > > >
> > > > it it not clear what you did.
> > > >
> > > >
> > > > not sure why you are not getting any bonds.
> > > > you can try loading the .gro file and then
> do
> > > > mol bondsrecalc $mol
> > > > topo retypebonds
> > > >
> > > > that should trigger the internal flags in
> VMD
> > > > to write out bonds.
> > > >
> > > > you have to manually set any charges that
> are not
> > > > given through input in case you want them
> set in the
> > > .psf.
> > > >
> > > > you have to remember this is not psfgen
> where this is
> > > > all read from a parameter database, you are
> doing all
> > > > steps by hand.
> > > >
> > > > cheers,
> > > >    axel.
> > > >
> > > > p.s.: please turn off html format mails to
> mailing
> > > lists and always
> > > > keep the list in cc.
> > > > i usually don't respond to questions send to
> me
> > > directly that don't concern me
> > > > personally, or else i would have no time to
> get
> > > anything done. thanks.
> > > >
> > > >> However, when I added the Cl- manually
> the psf
> > > generation went well and loaded in VMD
> > > >>
> > > >> Thanks a lot for your help :)
> > > >>
> > > >> Rabab Toubar
> > > >>
> > > >>
> > > >> --- On Tue, 6/15/10, Axel Kohlmeyer
> <akohlmey_at_gmail.com>
> > > wrote:
> > > >>
> > > >> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > >> Subject: Re: vmd-l: top2psf.tcl
> > > >> To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > > >> Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> > > >> Date: Tuesday, June 15, 2010, 9:59 AM
> > > >>
> > > >> On Tue, Jun 15, 2010 at 9:49 AM, Rabab
> Toubar
> > > <rtoubar_at_yahoo.com>
> > > wrote:
> > > >> >
> > > >> > I need the .psf file as we have in
> house
> > > codes used for analysis and these use .psf and
> .dcd as in
> > > case of NAMD.
> > > >>
> > > >> > I tried to load the .gro or .pdb
> files and
> > > save coordinates as psf, but this is not an
> option in the
> > > drop down menu in vmd; is there a way I can do it
> in tcl?
> > > >>
> > > >> of course:
> > > >>
> > > >> animate write psf myfile.psf
> > > >>
> > > >> > I do have disulfide bonds- if this
> what you
> > > meant by unusual bonds.
> > > >> >
> > > >> > In the meantime I will try in
> gromacs to get
> > > the .top file from the .gro and see if this would
> work to
> > > get the .psf.
> > > >>
> > > >> one possible alternative (untested):
> > > >>
> > > >> #load .gro and .psf file into vmd
> > > >> set mol1 [mol new myfile.psf waitfor
> all]
> > > >> set mol2 [mol new myfile.gro waitfor
> all]
> > > >> set sel1 [atomselect $mol1 all]
> > > >> set sel2 [atomselect $mol2 water]
> > > >>
> > > >> # merge selections into new molecule.
> > > >> package require topotools
> > > >> ::TopoTools::selections2mol "$sel1
> $sel2"
> > > >>
> > > >> # write out new molecule
> > > >> animate write psf combined.psf
> > > >>
> > > >>
> > > >>
> > > >>
> > > >>
> > > >>
> > > >> > Thanks
> > > >> > Rabab Toubar
> > > >> >
> > > >> >
> > > >> > --- On Tue, 6/15/10, Axel Kohlmeyer
> <akohlmey_at_gmail.com>
> > > wrote:
> > > >> >
> > > >> > From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > >> > Subject: Re: vmd-l: top2psf.tcl
> > > >> > To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > > >> > Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> > > >> > Date: Tuesday, June 15, 2010, 9:29
> AM
> > > >> >
> > > >> > On Tue, Jun 15, 2010 at 9:21 AM,
> Rabab Toubar
> > > <rtoubar_at_yahoo.com>
> > > wrote:
> > > >> > >
> > > >> > > Thanks Axel for your reply
> > > >> > >
> > > >> > > My .top file has no waters, as
> it is the
> > > initial .top file I get using grompp, and it has
> a total of
> > > 357 atoms (attached).
> > > >> > >
> > > >> > > The md gro file has 11632, and
> it
> > > contains waters.
> > > >> >
> > > >> > well, you cannot load multiple
> files into the
> > > same VMD
> > > >> > "molecule" that have different
> number of
> > > atoms.
> > > >> >
> > > >> > > I can visualize the molecule
> using .pdb
> > > or .gro file with the .trr, but I need to have a
> psf files
> > > for further analyses, so can I possibly include
> waters in
> > > the top file? or may be delete it from the .trr
> file?
> > > >> >
> > > >> > what exactly do you need the .psf
> file for?
> > > >> >
> > > >> > the one generated from the .top
> file is only
> > > minimal
> > > >> > and only contains the bonding
> information and
> > > atom
> > > >> > names. that is suitable for
> visualization in
> > > VMD, but
> > > >> > not much more. in most cases, you
> can
> > > generate the
> > > >> > same kind of file by loading a .gro
> or .pdb
> > > file and saving
> > > >> > the result in a .psf file. only if
> you have
> > > unusual bonding,
> > > >> > you'd need to read it from the .top
> file.
> > > >> >
> > > >> > cheers,
> > > >> >     axel.
> > > >> >
> > > >> >
> > > >> >
> > > >> > >
> > > >> > > Thanks
> > > >> > > Rabab Toubar
> > > >> > >
> > > >> > >
> > > >> > > --- On Sun, 6/13/10, Axel
> Kohlmeyer
> > > <akohlmey_at_gmail.com>
> > > wrote:
> > > >> > >
> > > >> > > From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > > >> > > Subject: Re: vmd-l:
> top2psf.tcl
> > > >> > > To: "Rabab Toubar" <rtoubar_at_yahoo.com>
> > > >> > > Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> > > >> > > Date: Sunday, June 13, 2010,
> 8:19 AM
> > > >> > >
> > > >> > > > However when I load the
> psf file in
> > > vmd, I got the following:
> > > >> > > >
> > > >> > > > "psfplugin) WARNING: no
> angles
> > > defined in PSF file.
> > > >> > > > psfplugin) WARNING: no
> dihedrals
> > > defined in PSF file.
> > > >> > > > psfplugin) WARNING: no
> impropers
> > > defined in PSF file.
> > > >> > > > psfplugin) no cross-terms
> defined
> > > in PSF file.
> > > >> > > > Info) Analyzing structure
> ...
> > > >> > > > Info)    Atoms:
> 357
> > > >> > > > Info)    Bonds:
> 365
> > > >> > > > Info)   
> Angles: 0  Dihedrals:
> > > 0  Impropers: 0  Cross-terms: 0
> > > >> > > > Info)   
> Bondtypes: 0
> > > Angletypes: 0  Dihedraltypes: 0 
> Impropertypes: 0
> > > >> > > > Info)   
> Residues: 36
> > > >> > > > Info)   
> Waters: 0
> > > >> > > > Info)   
> Segments: 1
> > > >> > > > Info)   
> Fragments: 1 
> > > Protein: 1   Nucleic: 0"
> > > >> > >
> > > >> > > that is to be expected after
> the debug
> > > output from above.
> > > >> > >
> > > >> > > > And when I load the trr
> file from
> > > GMX, I get the following:
> > > >> > > >
> > > >> > > > "ERROR) BaseMolecule:
> attempt to
> > > init atoms while structure building in progress!
> > > >> > > > ERROR) Invalid number of
> atoms in
> > > file: 11632
> > > >> > > > Info) Using plugin trr
> for
> > > coordinates from file
> /home/Desktop/gmx/pr_md_1.trr
> > > >> > > > ERROR) Incorrect number
> of atoms
> > > (11632) in
> > > >> > > > ERROR) coordinate file
> > > /home/Desktop/gmx/pr_md_1.trr
> > > >> > > > Info) Finished with
> coordinate file
> > > /home/Desktop/gmx/pr_md_1.trr."
> > > >> > >
> > > >> > > either the .trr file doesnt
> match the
> > > .top file, or there is something
> > > >> > > else wrong, that is impossible
> to debug
> > > without having access
> > > >> > > to those files. have you tried
> loading a
> > > matching.gro file?
> > > >> > > how many atoms does it have?
> > > >> > >
> > > >> > > cheers,
> > > >> > >   
>    axel.
> > > >> > >
> > > >> > > > PS I am using the
> preprocessed top
> > > file like Axel suggested in an earlier post
> > > >> > > >
> > > >> > > > Any suggestions would be
> much
> > > appreciated
> > > >> > > > Thanks
> > > >> > > > Rabab Toubar
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > > --
> > > >> > > Dr. Axel Kohlmeyer 
>   akohlmey_at_gmail.com
> > > >> > > http://sites.google.com/site/akohlmey/
> > > >> > >
> > > >> > > Institute for Computational
> Molecular
> > > Science
> > > >> > > Temple University,
> Philadelphia PA,
> > > USA.
> > > >> > >
> > > >> > >
> > > >> >
> > > >> >
> > > >> >
> > > >> > --
> > > >> > Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> > > >> > http://sites.google.com/site/akohlmey/
> > > >> >
> > > >> > Institute for Computational
> Molecular
> > > Science
> > > >> > Temple University, Philadelphia PA,
> USA.
> > > >> >
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> > > >> http://sites.google.com/site/akohlmey/
> > > >>
> > > >> Institute for Computational Molecular
> Science
> > > >> Temple University, Philadelphia PA,
> USA.
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> > > > http://sites.google.com/site/akohlmey/
> > > >
> > > > Institute for Computational Molecular
> Science
> > > > Temple University, Philadelphia PA, USA.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> > > http://sites.google.com/site/akohlmey/
> > >
> > > Institute for Computational Molecular Science
> > > Temple University, Philadelphia PA, USA.
> > >
> >
> >
> >       
> >
>
> --
> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>