[gmx-users] genbox

Stud_Psychopharm stu_psyc at nimhans.kar.nic.in
Wed Aug 18 18:29:59 CEST 2004

dinesh, you can add water molecules by  using genbox command. After that 
just remove the unwanted water molecules by writing a small program. ie 
just define the coordinate values and after that point if any water 
molecule is present, just ask the program to delete those from the pdb 
file.. so that you can get the desired number of water mols.
blaise m costa.

"The more we learn the more we realize how little we know." - 
R.Buckminster Fuller 

Blaise M.
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.

-----Original Message-----
From: Dinesh Pinisetty <dpinis1 at lsu.edu>
To: gmx-users at gromacs.org
Date: Fri, 13 Aug 2004 11:09:49 -0500
Subject: [gmx-users] genbox

> Respected users,
>          I have two questions they might look silly but as i am a
> beginner
> it is very important for me to know answers to them...
> 1)I have taken a molecule of DPPC and created a
> bilayer on my own using genconf and editconf
> commands.Now before doing Energy minimization I want
> to add water and then perform energy minimization.If I
> am using genbox command to add water molecules it adds
> 64,245 molecules which is very very high number,I want
> to add 60 per molecule of DPPC I have 96 DPPC
> molecules,i.e I want to add 96*60 5760 molecules,how
> to have control on adding water molecules in the box.I
> heard from Dr.ANTON FEESTRA that genbox adds water molecules basing on
> box
> size my box size is just above half the cut-off which is a requirement
> i.e.
> even my box size is not so large(I used -d 0.75 in editconf).
>        In the pdb file of Dr.Tielmann's site water molecules are
> present
> did they add them using genbox if so how could they control the number?
> 2) My second question is if I also want to add sugars
> etc in the system,can I do that using the pdb file I
> have downloaded from Dr.Tielmann's site.I mean how to control the x,y,z
> co-ordinates while adding. The pdb file in Dr.Tielman's site when
> visualized water is outside of the membrane on both sides similarly I
> want
> to add sugars
> on both sides along with water but how to see that
> co-ordinates of the sugar atoms make them to settle
> along with water outside the bilayer.
> Please let me know answers for the above questions,I would be grateful
> to
> you if you could answer me the above
> questions......
> Thanking you,
> Dinesh Pinisetty.
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