how to apply restraints for phi and psi for alpha helix regions

From: Achani K. Yatawara (Achani.K.Yatawara_at_Dartmouth.edu)
Date: Thu Dec 11 2008 - 07:42:37 CST

Hi everyone,

Sorry for asking the same question again. I am a new NAMD user and I hope NAMD experts can help me with the following problem.

I want to apply phi and psi restraints for 2 alpha helix regions for initial steps of my simulation.

 I tried the way given in the users guide pages 82-89, considering free energy of conformational change calculations, applying fixed restraints for phi and psi dihedral angles for the necessary helix regions.
However I got an error massage as "invalid atomID" etc.
Part of my conf. file is as follows,

freeEnergy on
freeEnergyConfig {

urestraint {

dihe group { ( C, N, CA, C ): ( P, 2 ) to ( P, 10 ) }
         group { ( C, N, CA, C ): ( P, 17 ) to ( P, 30 ) barr=20 ref=-57
 }
 
urestraint {
dihe group { ( N, CA, C, N ): ( P, 2 ) to ( P, 10 ) }
         group { ( N, CA, C, N ): ( P, 17 ) to ( P, 30 ) } barr=20 ref=-47
     
}
}

Error massage :
FreeEnergy: Problem parsing input parameters
FreeEnergy: Error: Invalid AtomID
FreeEnergy: Read Until: ( p, 2 ) to ( p, 10 ) }
        
        group { ( c, n, ca, c ): ( p, 17 ) to ( p, 30 ) } barr=20 ref=-57
 }
 
urestraint {
dihe group { ( n, ca, c, n ): ( p, 2 ) to ( p, 10 ) }
         group { ( n, ca, c, n ): ( p, 17 ) to ( p, 30 ) } barr=20 ref=-47
     
}

FreeEnergy:
FATAL ERROR: FreeEnergy: Fatal Parsing Error

Does anyone have a correct way to do this ? All suggestions are highly appreciated.

Thank you in advance for your valuable time and attention.

Achani Yatawara

email: Achani.K.Yatawara_at_Dartmouth.edu

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