VMD-L Mailing List

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Nov 21 2006 - 11:39:53 CST

Now I have tried using "mol load".
vmd load the molecule, but it can't recognize "waitfor"

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