[gmx-users] Removing water molecules from inside of the protein

[Justin A. Lemkul]

DimitryASuplatov wrote:
> Hello,
> recently after adding spc water to a structure I have notice that the
> molecules have been added to internal cavities. Even though this
> situation is possible, for example water could get inside during
> folding, this could cause artificial movement of aminoacids being
> pushed from inside by internal water. I have also noticed that if I
> trjconv gro file to pdb (for use in pymol editor) all solvent
> identificators change and that makes them untraceable.
> Is there a known program to remove internal solvent molecules? Do you
> think its crucial?
> 

You can get rid of them with a text editor, if you know their residue numbers, 
or change the VDW radius of C or N slightly to try to exclude more water during 
the genbox stage.

Also, editconf is better suited for .gro-->.pdb conversion (and vice versa).

-Justin

> Thanks.
> SDA
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================