From: Eric Hajjar (ericha_at_ii.uib.no)
Date: Fri Jul 30 2004 - 02:45:05 CDT
Hi all,
I want to add ions to a macromolecular system as to be able to lanch
molecular dynamics with NAMD (need neutrality with PME, even if
interestingly no particular behavior are seen with a charged system...) .
I was using "Sodium" until now but it seems to crash for ion > 3 !
The best is to use "wat2ions", that take as input a Delphi-potential map
( file .phi).
The problem is that Delphi (as to save space ?) provide with a binary .phi
file format, and wat2ions need the file to be in ASCII...
I'm going throught the manual again and there is hints for writing a
program that converts phi to ascii and vice & versa, but I wonder if one
of you had the same need before, if there is already such a converter
(ASCIIPHI ?), or how you went through such a "problem"...
Perhaps this mail would be more for the VMD-mailing list , but adding ions
is in principle a typical "system-setup" for MD simulation...
Any help is appreciated
Thanks in advance.
Eric Hajjar
Phd Student @University of Bergen
Computational Biology Unit
BCCS/UNIFOB, Bergen, NORWAY
mail:ericha_at_ii.uib.no
tel:(+47)55584029
> Emil Alexov, Senior Scientist, HHMI
> Black Building, Room 221, Biochemistry Department
> Columbia University, 630W 168 Street, New York 10032
> Tel: (212) 305 0265, Fax: (212) 305 6926
>
>
-- Eric Hajjar Phd Student @University of Bergen Computational Biology Unit Molecular Modeling Group BCCS/UNIFOB, Bergen, NORWAY mail:ericha_at_ii.uib.no tel:(+47)55584029
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