delete water residues: mangled atom specifier
I’m running an amber trajectory and in particular snapshots I’d like to delete all water molecules but one. If I do del :WAT !1355.water I get a “mangled atom specifier”. Obviously I got the wrong syntax. Your help will be much appreciated Regards George
Hi George, You need something more like: del :wat & ~ :1355.water (delete wat residues AND NOT residue 1355 in water chain) I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 6, 2014, at 2:02 PM, George Tzotzos <gtzotzos@me.com> wrote:
I’m running an amber trajectory and in particular snapshots I’d like to delete all water molecules but one.
If I do
del :WAT !1355.water
I get a “mangled atom specifier”. Obviously I got the wrong syntax. Your help will be much appreciated
Regards
George
Hi Elaine, Many thanks. Your help is greatly appreciated. Regards George On 6Oct, 2014, at 7:30 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, You need something more like:
del :wat & ~ :1355.water
(delete wat residues AND NOT residue 1355 in water chain)
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 6, 2014, at 2:02 PM, George Tzotzos <gtzotzos@me.com> wrote:
I’m running an amber trajectory and in particular snapshots I’d like to delete all water molecules but one.
If I do
del :WAT !1355.water
I get a “mangled atom specifier”. Obviously I got the wrong syntax. Your help will be much appreciated
Regards
George
participants (2)
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Elaine Meng -
George Tzotzos