AMBER Archive (2006)

Subject: Re: AMBER: water molecules with in 3 angstroms to the solute

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jan 03 2006 - 18:40:07 CST


Dear Nagaraju,

U can check out the following website for more info on VMD Selection
Methods.

http://www.ks.uiuc.edu/Research/vmd/current/ug/node76.html

Load the structure in VMD, and then from VMD Main Window;

Graphics > Representations

A new window called 'Graphical Representations' will popup. By pressing
Create Rep, u can create a new representation. What this does is, it will
create a new layer with the properties u are will give in the 'selected
atoms' command line.

So, for instance let's say we have a RNA, which is solvated in
water (as it is the case in the attached deneme.pdb file). Load this
structure. In 'Graphical Representation' window, you will have only one
representation (layer). You can create as many layers as you want, and the
layers will overlap in the DISPLAY window which shows the selected atoms.
I am going to use one layer for the case you are interested. In the
'selected atoms' part, write the following:

(water within 3 of resid 1 to 8) or (all not water)

As it is obvious from this line, it is choosing both the atoms which are
not water or the water molecules which are 3A away from resid 1-8 (which
is just the RNA). The reason why I used the resid rather the word
'nucleic' is because sometimes VMD does not understand if the residue is
part of nucleic acid or not. When u check out the .pdb file, u will see
that I have RG5 in it. And VMD wont understand that this is a nucleic
acid. In any case, if your structure was created by residues named
RC,RG,RU,RA,DC,etc., the word 'nucleic' would have chosen all of the atoms
of the RNA (or DNA). For more information, check out the above website I
wrote.

In order to save the current atoms in a file like .pdb or .crd, go to the
VMD Main window. Select the molecule (here, it is deneme.pdb) and then

File > Save Coordinates

This will popup a new window called 'save trajectory'. The 'Selected
atoms' part is empty. So, click on the icon just right to that empty
line, and choose which layer(representation) u want to save. Then choose
the file type, etc. etc. and u will be able to save the structure in a
.pdb or .crd file. I have saved the structure in a file called sonuc.pdb
(attached).

I hope this helps. For more information on how to use VMD, I would
strongly suggest to use their website.

Good luck.

On Tue, 3 Jan 2006, nag raj wrote:

> Dear Ilyas,
> Thank you for your relpy. Would you help
> me, i have one more doubt. How to get molecule in
> "pdb" or in "crd" formate which contains water
> molecules with in 3angstroms. Once again thank you for
> your reply.
> bye
> nagaraju
>
> --- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
>
> > Dear Nagaraju,
> >
> > If you just want to see the structure with water
> > molecules that are 3A
> > within your structure, you can use VMD to do that.
> > You need to play with
> > the representation part of VMD. Check out the VMD
> > website for that.
> >
> > Good luck,
> >
> > On Mon, 2 Jan 2006, nag raj wrote:
> >
> > > Dear Amber users,
> > > I solvated the solute with
> > water
> > > (TIP3P) solvent, buffer radious is 10 angstroms.
> > After
> > > MD simulations, i want to see water molecules
> > within 3
> > > angstroms to the solute. Would you tell me how to
> > do
> > > this.
> > > Thank you in advance.
> > > Happy new year.
> > >
> > > bye
> > > Nagaraju
> > >
> > >
> > >
> > > __________________________________________
> > > Yahoo! DSL Something to write home about.
> > > Just $16.99/mo. or less.
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> > >
> > >
> >
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> > --
> > Ilyas Yildirim
> >
> >
> ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67
> > 66 (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
> >
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------



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