VMD-L Mailing List

From: Stephen M. Dutz (smdutz_at_csupomona.edu)
Date: Wed Feb 21 2007 - 15:40:45 CST

Hi, I'm somewhat new to VMD and am attempting to create a
protein-membrane system. After implanting the protein in the POPC I try
to solvate it only on the hydrophilic ends using VMD's solvate package.
However, I seem to have the same problem others have had with waters
appearing along the hydrophobic sides. After looking through the
mailing list I found this tcl script which some of you have used for
this exact issue (courtesy Marcos Sotomayor). After customizing it for
my system I end up with this:

 

package require solvate

solvate cff2_mem.psf cff2_mem.pdb -o yourprotein_water_TEMP -b 3.5
-minmax {{-55 -55 -50} {5 5 50}}

set all [atomselect top all]

$all set beta 0

set seltext "segid WT1 to WT99 and same residue as abs(z) <10"

set sel [atomselect top $seltext]

$sel set beta 1

set badwater [atomselect top "name OH2 and beta > 0"]

set seglist [$badwater get segid]

set reslist [$badwater get resid]

mol delete all

package require psfgen

readpsf yourprotein_water_TEMP.psf

coordpdb yourprotein_water_TEMP.pdb

foreach segid $seglist resid $reslist {

delatom $segid $resid

}

writepdb yourproteinw.pdb

writepsf yourproteinw.psf

file delete yourprotein_water_TEMP.psf

file delete yourprotein_water_TEMP.pdb

exit

 

However when I run it I keep generating this error:

 

Solvate 1.2 completed successfully.

There is no 'top' molecule in atomselect's 'molId'

can't read "all": no such variable

segid WT1 to WT99 and same residue as abs(z) <10

There is no 'top' molecule in atomselect's 'molId'

can't read "sel": no such variable

There is no 'top' molecule in atomselect's 'molId'

can't read "badwater": no such variable

can't read "badwater": no such variable

ERROR) No molecules loaded.

1.4.4

reading structure from psf file yourprotein_water_TEMP.psf

 

reading coordinates from pdb file yourprotein_water_TEMP.pdb

can't read "seglist": no such variable

 

I'm confused as to what it is saying with the 'no top molecule'. When I
load the pdb into vmd it shows that it is selected as the 'top'
molecule. Any help is much appreciated.

 

-Steve