VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Jun 15 2010 - 11:22:55 CDT

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]

# 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

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.
>