Re: membrane tutorial.

From: Francesco Oteri (
Date: Wed Sep 22 2010 - 15:49:38 CDT

  The correct sintax is "same residue as (z>10 and z <-10)", excuse me
for the wrong syntax.
The value has been chosen using the lipid z limits, and carefully
visually inspecting the atoms. If you put the comands between quotes in
a Representation (without the "not" clause), you will visualize the
selected atoms.
Eg: same residues as (z>10 and z <-10) will visualize the atoms you want
to exclude.

The exclusin will be applied when you'll save using the "not" word
during the saving.

I do the exclusion, before starting the minimization. The problem i
found is at the interface between protein and lipids because i removed
at the same manner the lipids
too close to the protein. The deletion of the lipids, give rise a empty
space but, luckily, the problem was solved during equilibration.

Il 22/09/2010 12:09, Swarna M Patra ha scritto:
> Hi
> is it same residue or same residue as? after step1 (fix atom, min) you
> do this? the value < -10 and > 10 are the zmin and zmax of lipid
> right? or how do you come up with that no?
> On Wed, Sep 22, 2010 at 1:54 PM, Francesco Oteri
> < <>> wrote:
> Hi Swarna,
> you need to push water to avoid the presence of water molecules
> within the membrane.
> Hi solved the problem without pushing water. I removed the waters
> molecules with the following vmd command:
> [atomselect top "not (same residue (z>10 and z <-10))"] writepsf
> memb.psf
> [atomselect top "not (same residue (z>10 and z <-10))"] writepdb
> memb.pdb
> In this way I've selected the water into the membrane basing on
> their z position and saved a file without them.
> On 22/09/2010 08:44, Swarna M Patra wrote:
>> Hi Namd users,
>> I am looking at the files of *Membrane Proteins Tutorial. I dont
>> find a1b2c5_init.pdb can any one tell me what this file contains
>> where I can get it. And how to select these water residue no in
>> except water selection in keep_water_out.tcl script. I looked at
>> the gramicidin tutorial also. why the lipid tail melt is done in
>> gramacidin and also water push . is water push essential?
>> thanks
>> swarna
>> *

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