From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Jun 10 2010 - 04:00:41 CDT
Dear NAMD community,
> We are attempting to perform a replica exchange molecular dynamics (REMD)
> simulation with NAMD2.7b2. We started with the alanin folding example, using
> the *given* .psf, .pdb and the alanin.params file.
> After that, we generated a .psf using psfgen and CHARMM topology
> (top_all22_prot_cmap.inp), and attempted to rerun REMD in the same way
> (using namd_replica_server.tcl, replica_exchange.tcl, and spawn_namd.tcl)
> using par_all22_prot_cmap.inp. This time, however, the simulations did not
> run, and we get the foll. messages in each log file:
> FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE
> LINE=**>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<*
> We are not sure how to get over this problem. Do we really need to change
> the formats in the parameter file to match that in alanin.params?
> We would appreciate some help in this regard.
> Thank and regards,
> Neelanjana Sengupta
> ps: The alanin.params file is attached with this email.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:51 CST