VMD-L Mailing List

From: John Grime (jgrime_at_uchicago.edu)
Date: Mon Nov 11 2013 - 09:04:24 CST

Hello,

I'm trying to create a large solvation box using VMD 1.9.2a33 for Linux/AMD64, and while the solvation script appears to work, VMD is unable to load the resultant PDB file.

The "solvate.psf" file appears to be okay, but the "solvate.pdb" file produces the following error when read into VMD:

Info) Using plugin pdb for coordinates from file /home/solvate.pdb
ERROR) Incorrect number of atoms (10445941) in
ERROR) coordinate file /home/solvate.pdb

There should be around 50,000,000 atoms in the PDB file (this value is correctly reported when reading "solvate.psf").

Can anyone help me to figure out what I can do, here?

Also, the topology file which seems to accompany the solvate plugin has a somewhat different set of data for the TIP3 water compared to the contents of "toppar_water_ions.str" in the CHARMM36 force field set that I'd like to use. As the difference seems to only be the presence of "DONOR" entries in "toppar_water_ions.str" ("wat.top" in the solvate plugin only has an "ACCEPTOR" entry), I guess this difference is not significant as NAMD typically ignores thes H-bond entries?

Thanks!

J.