Re: [AMBER] Dimension Box visualization

From: Matias Machado <>
Date: Thu, 31 May 2018 08:45:13 -0300 (UYT)

Dear Aashish,

Adding to David's answer...

The system may be too big to fit the file format rst7 (my_solv.inpcrd), indeed it is always recommended to use NetCDF format (binary) for restart and trajectories.

In addition, if you don't mind about the initial position of the ions, you may place them randomly by replacing water molecules instead of using to the electrostacic potential... it's a quite faster method!

source leaprc.ff14SB.redq
mol=loadpdb my.pdb
solvatebox mol TIP3PBOX 15
addIonsRand mol Na+ 202
addIonsRand mol Cl- 202
saveAmberParmNetcdf mol my_solv.prmtop
savepdb mol my_solv.pdb



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "David A Case" <>
Para: "AMBER Mailing List" <>
Enviados: Jueves, 31 de Mayo 2018 8:29:35
Asunto: Re: [AMBER] Dimension Box visualization

On Thu, May 31, 2018, Aashish Bhatt wrote:
> I need to perform dynamics for a protein complex. For this i tried making
> the topology and coordinate file. When i visualized topology file and pdb
> file in VMD, Dimensions of the box are not cubic(attached files).

I see two issues here:

1. The solvateBox command will not make a cubic system, but rather a
rectangular parallelopiped (hope that's the right term!), with different
lengths on each side. (Maybe that is what you meant.)

2. The VMD visualization problem comes from limitations in the old PDB
format, which cannot (easily) describe more than 100,000 atoms or 10,000
residues. The are various non-standard workarounds to this problem, and
VMD seems not to recognize what Amber does.

Try loading the prmtop and and initial coordinate (restart) file into

...good luck...dac

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