VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 15 2010 - 12:00:00 CDT

On Tue, Jun 15, 2010 at 12:57 PM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
> Axel, when I try to set the last selection to "set sel3 [atomselect $mol2 ion]" I get no ions in the

please RTFM about atomselect and look at the VMD tutorials.

as i said, it is a case of PEBCAC.

a.

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.
>>
>>
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.