AMBER Archive (2009)

Subject: [AMBER] How to keep the closest solvent mols to each atoms by PTRAJ?

From: u8613020_at_msg.ndhu.edu.tw
Date: Thu Aug 06 2009 - 20:40:17 CDT

Dear all,
Is there any way to use PTRAJ to output the closest solvent molecules, i.e., 100 water moleculaes,
of several selected heavy atoms instead of the center of mass of several selected heavy atoms?
(I found the closest 100 water are around the center of mass of the selected atoms in the mask
instead of each atom the selected atoms in the mask)
Thank you!

#####This is the PTRAJ input script I used:
trajin ./complex.ALLwater.restrt.Z
trajout ./complex.100water.restrt
closestwater 100 @OH6,@OH5,@OH4,@OH3,@OH2,@OH1,@C9,@C8,@C7,@C6,@C5,@C4,@C3,@C2,@C1,@N3,@N2,@N1 first
go

Sincerely,
yuann

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