VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 27 2018 - 11:04:24 CDT

If you use solvate via the scripting interface, you can make it
emit other file formats besides PDB. This is necessary when building
huge systems will millions or billions of atoms, for example:
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/largesystems/

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 27, 2018 at 09:26:31PM +0530, Mani Kandan wrote:
> Yes, I tried to create a water box of size ranges from (2000,2000,2000 to
> 1800, 1800,1800). But Still, I am getting the error. If the PDB format
> restricts then, is there any other way to do.
> Regards,
> MANIKANDAN D
> On Mon, Aug 27, 2018 at 6:26 PM Vermaas, Joshua
> <[1]Joshua.Vermaas_at_nrel.gov> wrote:
>
> PDB files are formatted in a rather unfortunate way. The format doesn't
> fit atoms whose values fall outside the range (-999.999, 9999.999). With
> the big box you've made, the pdb can't be written, since it exceeds the
> size for the field (probably). Move your initial structure's center to
> 1000,1000,1000 in the input pdb, and try again.
>
> -Josh
> Â
> Â
>
> On 2018-08-27 04:22:05-06:00 [2]owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Dear all,
> Â Â Â Â Â Â Â Â Â Â Â Â Â Â When I solvating my system for large
> dimensions, I am getting following errors in the vmd.Â
> psfgen) Info: writing pdb file sin_sol_spce.pdb
> psfgen) Info: pdb file complete.
> psfgen) clearing structure, preserving topology and aliases
> atomsel: writepdb failed.
> I am using following comment for solvating purpose:
> package require solvate
> solvate sin_channel_charges_modified.psf
> sin_channel_charges_modified.pdb -z 1000 +z 1000 -s W -o sin_sol_spce
> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Kindly, help me in these regard.
> With Regards,
> MANIKANDAN D
>
> References
>
> Visible links
> 1. mailto:Joshua.Vermaas_at_nrel.gov
> 2. mailto:owner-vmd-l_at_ks.uiuc.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/