VMD-L Mailing List

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Thu Dec 15 2011 - 16:58:43 CST

Axel,
        That's exactly the type of thing I was hoping to hear. Thanks again,

rajan

On Thu, 2011-12-15 at 17:38 -0500, Axel Kohlmeyer wrote:
> On Thu, Dec 15, 2011 at 5:30 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> > Dear Axel,
> > Thanks for your response. This is the function I need:
> > set combined [TopoTools::mergemols "$solute $solvent"]
> > However, because I use an instance of VMD that is installed on the MSI
> > supercomputing center, I have to wait for stable releases of the VMD
> > client. I'm looking forward to the topotools package updates being
> > included into the next stable release because it seems that the
> > mergemols routine will be useful.
>
> there is no problem installing a different version
> of vmd by yourself in your home directory. VMD
> doesn't need any superuser privileges.
>
> even more so, you can just download the topotools
> 1.2 snapshot, install it somewhere and then alter
> your .vmdrc file to include the directory in the search
> path (that is what i and many others use for development
> of plugins).
>
> axel.
>
> > In order to solvate the molecule, I simply used the Merge script from
> > the GUI's "Extensions -> Modeling" to merge the two molecules together
> > into one set of files (one psf and one pdb). Then I used the command
> > set sel1 [atomselect top "segid TTH or (segid QQQ and (not same residue
> > as within 1.5 of segid TTH))"]
> > although it seems that I could have used the "exwithin" keyword to write
> > the same command more concisely.
> >
> > Thanks again,
> >
> > Rajan
> >
> > On Tue, 2011-12-13 at 15:16 -0500, Axel Kohlmeyer wrote:
> >> rajan,
> >>
> >> how about using this script (just whipped together in a few minutes)?
> >>
> >> this can be run in textmode, but you have to install
> >> a recent alpha test version of VMD or update the
> >> topotools plugin with the latest version from here:
> >>
> >> http://sites.google.com/site/akohlmey/software/topotools#TOC-Installation
> >>
> >> you cannot have a selection that crosses multiple molecules,
> >> but can easily combine multiple molecules, even if the atoms
> >> overlap and *then* detect the overlapping atoms using "exwithin"
> >> and make it remove entire molecules with "same fragment as".
> >>
> >> HTH,
> >> axel.
> >>
> >> =============================
> >>
> >> #!/usr/local/bin/vmd -e
> >>
> >> package require topotools 1.2
> >>
> >> # minimum required distance between atoms
> >> set mindist 2.5
> >>
> >> # load both molecules
> >> set solute [mol new TerthioPSFGEN50_D.psf waitfor all]
> >> mol addfile MDRun50_D.pdb mol $solute waitfor all
> >>
> >> set solvent [mol new 3cBoxCH2Cl2.psf waitfor all]
> >> mol addfile 3cEqOPLSCH2Cl2.pdb mol $solvent waitfor all
> >>
> >> set combined [TopoTools::mergemols "$solute $solvent"]
> >>
> >> # transfer box dimensions, if available.
> >> molinfo $combined set {a b c alpha beta gamma} [molinfo $solvent get
> >> {a b c alpha beta gamma}
> >>
> >> set sel [atomselect $solute all]
> >> # define a macro that make it easy to determine the solute
> >> atomselect macro solute "index < [$sel num]"
> >> $sel delete
> >>
> >> set sel [atomselect $combined "not (same fragment as (exwithin
> >> $mindist of solute))"]
> >> $sel writepsf merged.psf
> >> $sel writepdb merged.pdb
> >>
> >> # uncomment if run in text mode.
> >> #after 1000 {quit}
> >>
> >> ====================================
> >>
> >> On Tue, Dec 13, 2011 at 1:46 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> >> > Hi,
> >> > I have been trying to solvate a molecule with CH2Cl2 (the OPLS 3-site
> >> > model), but I haven't been able to get the solvate (version 1.3) plugin
> >> > to work. My problem is a bit easier than what the solvate plugin is
> >> > built for so I am constrained to this plugin.
> >> > Specifically, I have a molecule that I have minimized in vacuum. I know
> >> > the dimensions of this molecule (from minmax) so I created a solvent box
> >> > that would encompass the molecule with the solvent padding that I
> >> > wanted. Ideally I would like to merge the two pdb files together, and
> >> > have a simple algorithm to remove close contacts then writepdb and
> >> > writepsf. However, I cannot figure out a way to do this. Here's what I
> >> > have tried:
> >> > *****
> >> > Solvate plugin command:
> >> >
> >> > solvate TerthioPSFGEN50_D.psf MDRun50_D.pdb -o solvateD -s CU -minmax
> >> > {{-27.30 -27.30 -27.30} {27.3 27.32 27.32}} -x 0 -y 0 -z 0 +x 0 +y 0 +z
> >> > 0 -b 2 -spdb 3cEqOPLSCH2Cl2.pdb -spsf 3cBoxCH2Cl2.psf -stop
> >> > 3cEqOPLSCH2Cl2.top -ws 85.976 -ks {{type CH2}}
> >> >
> >> > My files are:
> >> > Solute PSF: TerthioPSFGEN50_D.psf
> >> > Solute PDB: MDRun50_D.pdb
> >> > Solvent PDB: 3cEqOPLSCH2Cl2.pdb
> >> > Solvent PSF: 3cBoxCH2Cl2.psf
> >> > Solvent topology file: 3cEqOPLSCH2Cl2.top
> >> > Side length of the cubic solvent box is: 85.976 A
> >> > Each solvent molecule has a segid of QQQ and only one atom of type CH2
> >> >
> >> > This plugin does not seem to work with my solvent because it either does
> >> > not encompass the solute with solvent as expected, and if I play around
> >> > with the -ws or any of the other dimensions to make the
> >> > solvent encompass the solute, I get an error telling me about a bug.
> >> > This error comes up (I believe) exclusively when the solvent box is
> >> > replicated in a periodic fashion. I have tried just about every
> >> > combination of the numerical values in the command line, and nothing
> >> > seems to work.
> >> >
> >> > *****
> >> > Outside of the solvate.tcl script, I've tried a simple scripting
> >> > attempt:
> >> >
> >> > It seems that the operative line in the solvate.tcl script is:
> >> > set sel [atomselect top "segid QQQ and $keysel and same residue as \
> >> > (x < $xmin or x > $xmax or \
> >> > y < $ymin or y > $ymax or \
> >> > z < $zmin or z > $zmax or \
> >> > within $rwat of (not segid QQQ))"]
> >> >
> >> > so I tried to duplicate the "within" portion of this. What I realized is
> >> > that I think it is impossible to get two different IDs to interact with
> >> > each other.
> >> > I first loaded VMD with the command:
> >> > vmd MDRun50_D.pdb TerthioPSFGEN50_D.psf
> >> > and then I loaded the files 3cEqOPLSCH2Cl2.pdb and 3cBoxCH2Cl2.psf with
> >> > the "new molecule" GUI tool. This gave me the solute (MDRun50_D.pdb with
> >> > ID 0) and the solvent (3cEqOPLSCH2Cl2.pdb with ID 1) in the same VMD
> >> > Main window.
> >> > Is there any way that I can write the command:
> >> > set sel [atomselect 1 "within 2 of molid 0"]
> >> > in some other fashion? In the solvate.tcl script, line:
> >> > within $rwat of (not segid QQQ)
> >> > seems to be doing exactly what I need, but because the two PDBs are in
> >> > different IDs, I cannot use the same syntax. Am I stuck merging the
> >> > files by hand and then doing this elimination myself? I'll post all the
> >> > relevant files on
> >> > http://www.tc.umn.edu/~rajan/VMD-l.html
> >> > in a few minutes.
> >> >
> >> > Thanks for any help I can get.
> >> >
> >> > Rajan
> >> >
> >>
> >>
> >>
> >
>
>
>