VMD-L Mailing List

From: Satyavani Vemparala (vani_at_VITAE.CMM.UPENN.EDU)
Date: Tue Feb 17 2004 - 16:48:51 CST

Hi!

I have made the following changes to the script that you sent me. i
removed the water part as iam planning to add the strips of water and then
equilibriate. I am getting some errors:

(1) the atoms are displaced. i was assuming that by giving t "0 0 0", the
atoms would not be displaced. e.g.,
Before script:
-------------
ATOM 1 C1 OLEO 1 25.238 -18.360 17.677 0.00 0.00 L001
ATOM 2 O1 OLEO 1 24.822 -17.975 16.590 0.00 0.00 L001

After Script:
-----------
ATOM 1 C1 OLEO 1 20.652 -21.504 -18.456 1.00 0.00 L001
ATOM 2 O1 OLEO 1 20.521 -20.344 -18.821 1.00 0.00 L001
 

(2) some of the hydrogens have (0,0,0) as coordinates

is there a mistake iam doing in the script? the lipid is DOPC, hence OLEO
& PCGL residues.

================================================================
package forget
package require psfgen 1.3

topology top_all27_lipid

mol load pdb dopc_only.pdb

set lipidsegs1 [[atomselect top "name N and z < 0"] get segid]
set lipidsegs2 [[atomselect top "name N and z > 0"] get segid]
set lipidsel1 [atomselect top "segid $lipidsegs1"]
set lipidsel2 [atomselect top "segid $lipidsegs2"]

set tl ""
lappend tl "0 0 0"

set sl "$lipidsel1 $lipidsel2"

set lid 1

foreach lipidsel $sl {
 foreach t $tl {
  $lipidsel moveby $t

  set oldsegs [lsort -unique [$lipidsel get segid]]
  foreach s $oldsegs {
    set segid [format "L%03d" $lid]
    incr lid

    set segsel [atomselect top "segid $s"]
    $segsel set segid $segid
    $segsel delete

    segment $segid {
      auto none
      first NONE
      last NONE
      residue 1 OLEO
      residue 2 PCGL
      residue 3 OLEO
    }
    patch EST1 $segid:2 $segid:1
    patch EST2 $segid:2 $segid:3
  }

  $lipidsel writepdb lipids.pdb.tmp
  coordpdb lipids.pdb.tmp
 }
}

regenerate angles dihedrals

writepsf dopc.psf
writepdb dopc.pdb

mol delete all

mol load psf dopc.psf pdb dopc.pdb

exit
====================================================================
On Mon, 16 Feb 2004, Jim Phillips wrote:

> Hi,
>
> The easy way is to use a Tcl foreach loop over all of your segments.
> I've attached a script I used to build a DPPC patch from similar input.
> There is some extra code to replicate the lipids, but otherwise this is a
> full example.
>
> Also, be sure to use "regenerate angles dihedrals" after building all of
> the lipid segments or you'll be missing several angles and dihedrals.
>
> -Jim