VMD-L Mailing List

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Mon Aug 27 2018 - 10:56:31 CDT

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 <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
>
>
>
> On 2018-08-27 04:22:05-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Dear all,
> When I solvating my system for large dimensions, I am
> getting following errors in the vmd.
> 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
> Kindly, help me in these regard.
> With Regards,
> MANIKANDAN D
>
>