VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Nov 21 2006 - 12:18:02 CST

On 11/21/06, Myunggi Yi <myunggi_at_gmail.com> wrote:
> Now I have tried using "mol load".
> vmd load the molecule, but it can't recognize "waitfor"

please read john's mail again. he asked you to use
'mol new' / 'mol addfiled' instead of 'mol load'
please check out the syntax of them in the VMD
user's guide.

axel.

>
>
> Info) Segments: 1
> Info) Fragments: 5285 Protein: 4 Nucleic: 0
> ERROR) Cannot read file of type waitfor
> Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> Info) Exiting normally.
>
>
> On 11/21/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> > Hi,
> > You'll want to add the text "waitfor all" at the end of each of
> > your "mol new" and "mol addfile" commands, which will cause VMD to
> > wait until structure/trajectory loading entirely completes before
> > it continues on and starts processing the rest of your script.
> > In general you want to use "mol new" rather than "mol load"
> > from now on...
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Nov 21, 2006 at 10:47:43AM -0500, Myunggi Yi wrote:
> > > Dear vmd users,
> > >
> > > I'm running a script using text mode.
> > >
> > > The script quit too early.
> > > The following is my script.
> > >
> > > vmd -dispdev text -eofexit < closest.scr > vmd.log
> > >
> > >
> > > ====closest.scr========
> > > source set-chain.tcl
> > > source closest.tk
> > > set sel1 [atomselect 0 "resname HMT"]
> > > set sel2 [atomselect 0 "noh and resid 27 to 37"]
> > > closest $sel1 $sel2 closest-hmt.dat
> > > =================
> > >
> > > ======set-chain.tcl===========
> > > # loading trajectory
> > > mol load parm7 hmt-in.parm7
> > > mol addfile org1-10.trj type crdbox first 250 last 999 step 1
> > > mol addfile org11-15.trj type crdbox
> > >
> > > # setup chain ID for helices
> > > [atomselect 0 "resid 1 to 27"] set chain A
> > > [atomselect 0 "resid 28 to 54"] set chain B
> > > [atomselect 0 "resid 55 to 81"] set chain C
> > > [atomselect 0 "resid 82 to 108"] set chain D
> > >
> > > # change resid according to the first unit
> > > foreach a_list [[atomselect 0 "chain A"] get resid] {
> > > set new_list [expr $a_list + 20]
> > > lappend res_list $new_list
> > > }
> > > [atomselect 0 "chain A"] set resid $res_list
> > > [atomselect 0 "chain B"] set resid $res_list
> > > [atomselect 0 "chain C"] set resid $res_list
> > > foreach a_list [[atomselect 0 "chain D"] get resid] {
> > > set new_list [expr $a_list - 61]
> > > lappend b_list $new_list
> > > }
> > > [atomselect 0 "chain D"] set resid $b_list
> > > ======================
> > >
> > > =========closest.tk=============
> > > # Usage: source closest.tk
> > > # set sel1 [atomselect 0 "resname HMT"]
> > > # set sel2 [atomselect 0 "noh and resid 27 to 37"]
> > > # closest $sel1 $sel2 closest-hmt.dat
> > >
> > > proc closest { sel1 sel2 file } {
> > > set fout [open $file w]
> > > set nf [molinfo [$sel1 molid] get numframes]
> > > set list1 [$sel1 list]
> > > set list2 [$sel2 list]
> > > set rilist [$sel2 get resid]
> > > set nlist1 [$sel1 get name]
> > > set nlist2 [$sel2 get name]
> > >
> > > # find distances between each pair
> > > for { set i 0 } { $i < $nf } { incr i } {
> > > $sel1 frame $i
> > > $sel2 frame $i
> > > set crd1 [$sel1 get {x y z}]
> > > set crd2 [$sel2 get {x y z}]
> > > set min 1000.0
> > >
> > > foreach atom1 $crd1 id1 $list1 {
> > > foreach atom2 $crd2 id2 $list2 {
> > > set dist [veclength [vecsub $atom2 $atom1]]
> > > if {$dist < $min} then {
> > > set min $dist
> > > set clidx1 $id1
> > > set clidx2 $id2
> > > }
> > > }
> > > }
> > > puts $fout "[expr ($i + 1)*10] [lindex $nlist1 [lsearch -exact
> > > $list1 $clidx1]] [lindex $rilist [lsearch -exact $list2 $clidx2]]
> > > [lindex $nlist2 [lsearch -exact $list2 $clidx2]] $min"
> > > }
> > > close $fout
> > > }
> > > ==================================
> > >
> > > This generated result with only a few snap shots.
> > >
> > > 10 H13 30 O 2.55249404907
> > > 20 H1 35 N 2.5135371685
> > > 30 H2 31 CA 2.72125959396
> > > 40 H1 35 N 2.57328534126
> > > 50 H12 31 O 2.73753976822
> > > 60 H9 31 OG 2.11878705025
> > >
> > >
> > > When I run "closest.tk" with GUI mode after loading trajectory,
> > > It worked and generated results with all snap shots.
> > >
> > > Do you have any idea?
> > > What is wrong with my script?
> > >
> > >
> > > --
> > > Best wishes,
> > >
> > > MYUNGGI YI
> > > ==================================
> > > KLB 419
> > > Institute of Molecular Biophysics
> > > Florida State University
> > > Tallahassee, FL 32306
> > >
> > > Office: (850) 645-1334
> > > http://www.scs.fsu.edu/~myunggi
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.