From: Radak, Brian K (bradak_at_anl.gov)
Date: Thu Jun 09 2016 - 14:16:46 CDT
It would seem that the RTF (topology) files that you loaded do not contain a residue definition for HFA. Did you provide one?
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov
________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of faride badalkhani [farideh.khamseh_at_gmail.com]
Sent: Thursday, June 09, 2016 9:27 AM
To: namd-l
Subject: namd-l: Building PSF for the system prepared by Packmol
Dear NAMD users,
I prepared a solvation box including a single dendrimer using Packmol. The solvent is fluoroalkane. I have PDB, PSF, Topology and Parameter file for solvent and solute, separately. When I get solvation box (PDB file) using Packmol I get the following error:
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) unknown residue type HFA
psfgen) extracted 8283 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown residue type HFA
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
which HFA is my solvent molecule.
Would you mind telling me how can I create PSF for solvent+solute?
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:32 CST