VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Aug 27 2018 - 07:56:56 CDT

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