Thank you sir its working
On Thu, May 31, 2018 at 5:15 PM, Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> 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 my_solv.rst.nc
> savepdb mol my_solv.pdb
> quit
>
> Best,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://www.pasteur.uy]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "David A Case" <david.case.rutgers.edu>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> 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
> VMD.
>
> ...good luck...dac
>
>
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Received on Tue Jun 05 2018 - 03:30:02 PDT
