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