Re: [AMBER] why no periodic information?

From: Aron Broom <>
Date: Wed, 18 Apr 2012 15:21:16 -0400

First, open your inpcrd file and go to the bottom and see if you actually
have a line describing the periodic conditions (lengths and angles). If
so, it's probably the way you opened it, an inpcrd file is not an AMBER
restart file, the restart file contains velocity information also. You
should open it as AMBER periodic coordinates, or something of the sort.
All those options should be right next to each other in VMD, so it's
surprising that you would have chosen the restart.

Also, I think you want to open the prmtop first, and then load the inpcrd
into that.


On Wed, Apr 18, 2012 at 3:16 PM, Albert <> wrote:

> Dear:
> 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
> _______________________________________________
> AMBER mailing list

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Wed Apr 18 2012 - 12:30:04 PDT
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