AMBER Archive (2009)

Subject: [AMBER] Solvate Box od amoeba water

From: Hemant Gangwar (hemant_at_physics.iisc.ernet.in)
Date: Fri Mar 06 2009 - 03:50:01 CST

---------------------------- Original Message ----------------------------
Subject: Solvate Box od amoeba water
From: "Hemant Gangwar" <hemant_at_physics.iisc.ernet.in>
Date: Fri, March 6, 2009 3:00 pm
To: amber_at_ambermd.org
--------------------------------------------------------------------------

I am using Amber10 . I am trying to Solvate Carbon nanotube(sp2 carbons)in
amoeba water using Sleap.I used following procedure
Source leaprc.amoeba
loadoff cnt.lib(lib file for CNT structure)
solvatebox DEN WATBOX 4
DEN is unit name for CNT & SP2 CARBON has been named as "CA" in cnt.lib file.
I got following error message

Warning: no amber force field has been loaded, VDW radii set to 1.5.
Though leaprc.amoeba loads amoebapro.prm file.
If I am trying to load other force field file than it says atom 202 &203
can not be identified.(atom 202 & 203 are amoeba water H & o ,defined in
amoebapro.prm).
thanks in advance. 

-- 
Hemant Gangwar
Graduate Student
Centre for Condensed Matter Theory
Indian Institute of Science
Bangalore
Mob-9632726167
www.physics.iisc.ernet.in/~hemant

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