[AMBER] why no periodic information?

From: Albert <mailmd2011.gmail.com>
Date: Wed, 18 Apr 2012 21:16:04 +0200

  I've built an md system with tleap by following command:

tleap -s -f leaprc.ff99SBildn
source leaprc.gaff
loadamberparams ligand_AC.frcmod
loadoff ligand_AC.lib
mol = loadpdb complex.pdb
solvatebox mol TIP3PBOX 11.0
charge mol
addions mol Na+ 42
addions mol Cl- 30
charge mol
set default FlexibleWater on
saveamberparm mol bm.prmtop bm.inpcrd

After than I open the solvated system in VMD:

new molecule --> bm.inpcrd (amber 7 restart)
load --> bm.prmtop (amber7 parm)

everything seems to be ok in VMD molecule viewer window. However, when I
try to open the periodic cell, nothing happen.... what I found is: all
Self, +x +y, +z are in the same position which responsible for that I
see "no periodic" cell because they overlap with each other......

I also try to type

pbc box

in VMD terminal, and it said:

-error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000).
Have you forgotten to set the pbc parameters?

Does anybody have any idea what happen?

thank you very much
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Received on Wed Apr 18 2012 - 12:30:04 PDT
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