freeEnergy parsing error

From: Lada Biedermannová (lada.biedermannova_at_img.cas.cz)
Date: Wed Apr 27 2011 - 09:08:46 CDT

Dear all,

I would like to perform the "Free Energy of Conformational Change"
type of calculation in NAMD. Specifically, I need to calculate a free
energy change of applying a harmonic restraint on a certain distance.

The problem is that my topology is in amber format. How can I specify
the segname for my molecule? I have tried both "{}" and "main" as
segname, but I keep getting parsing errors.

Could you please help me solve this problem?

Thanks in advance,
Lada Biedermannova

-----------------
Input:
-----------------

freeEnergy on
freeEnergyConfig {
 urestraint {
  dist ({}, 295, C) group {({}, 37, ND2), ({}, 108, NE1)} kf=10.0 ref=2.3
 }

 mcti {
  task = stepfade
  numsteps = 10
  equiltime = 10 ps
  accumtime = 100 ps
  print = 10 ps
 }
}

-----------------
Output:
-----------------

FreeEnergy: Problem parsing input parameters
FreeEnergy: Error: Can't Read Atoms
FreeEnergy: Read Until: ({}, 295, c) group {({}, 37, nd2), ({},
108, ne1)} kf=10.0 ref=2.3
 }

 mcti {
  task = stepfade
  numsteps = 10
  equiltime = 10 ps
  accumtime = 100 ps
  print = 10 ps
 }

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:52 CST