On Tue, May 21, 2013 at 6:56 AM, Rasha Alqus
<rasha.alqus.manchester.ac.uk>wrote:
> Dear Amber Users,
>
> I have but a macromolecule and put it in water box, how do I remove the
> water molecules that overlap with my macromolecules.
>
We do not have nearly enough information to provide targeted help here.
This is not an issue I typically encounter, since I use tleap to solvate
my systems. By default, I use a tleap script something like this (this is
a pseudo-script):
source leaprc.forcefield
sys = loadPDB my.pdb
solvateOct sys TIP3PBOX 15.0
addIonsRand sys Cl- 0 # if the system is positively-charged, Na+ if
negatively charged
saveAmberParm sys my.parm7 my.rst7
In this case, tleap does not put water atoms on top of the 'sys' atoms, so
I never have the problem you describe. If you are using amber software to
create your system, I suggest you follow a more conventional approach like
the one I described above. If you are not using Amber software, we are
unlikely to be able to provide much assistance (unless someone on this list
happens to use the same tool you do).
So in lieu of a more specific answer, here are a couple fixes:
1) Build your system so there are no overlaps
2) Write a script to remove the overlapping waters (obviously the
difficulty of this step depends in some degree on the file format you're
using, like PDB or mol2 or whatever)
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 21 2013 - 05:00:03 PDT
