From: Cavalleri A. (A.Cavalleri_at_soton.ac.uk)
Date: Mon Aug 17 2020 - 13:37:22 CDT
Hello NAMD users,
I'm a relatively new user to NAMD and VMD, and I've been encountering some issues with the psfgen binary in NAMD when constructing very large systems. The version of NAMD I am using is 2.13.
I'm following the exact instructions for setup found here:
http://www.ks.uiuc.edu/Research/vmd/minitutorials/largesystems/
I'm able to read the psf, coordinate the pdb file, and write the solvent.js file with the correct dimensions exactly as described, however, when I go back to check the file using 'readmol js' I encounter these errors:
Unable to add (duplicate?) residue WT1:1
ERROR: failed reading structure
I was under the impression that using the template and specifying the number of copies to make in each direction was the best way to construct large solvent systems. If anyone could give me some advice as to how I can resolve these errors, or an alternative method of construction, I would be very grateful. Here is a breakdown of the commands I have used:
/path/to/psfgen/ <<END
readpsf wat.psf
coordpdb wat.pdb
writemol js solvent.js n {x 0 0} n {0 y 0} n {0 0 z}
END
/path/to/psfgen/ <<END
readmol js solvent.js
END
I have tried running the exact same commands with the template files exactly s they are, i.e. without trying to copy them and enlarge the system in any other directions. In this case, there were no errors from the readmol command, so I think the issue lies when extending the system to make it bigger--_000_LNXP265MB138826E6501A917165972F73AB5F0LNXP265MB1388GBRP_--
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