Re: Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID"

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sat Sep 10 2005 - 17:49:26 CDT

I figured out my problem from below. The atomID is read from the .psf
file and not the .pdb file!

However, now I am still having problems. Everything is running fine, but
the restraint does not appear to be applied during minimization? Is there
anything I can do to apply the constraint during minimization?

I want to find the minimum energy structure with the dihedral constraint
with my force field at 0 K. However, the minimization appears to just
find the local minimum, although it does appear to be converging upon
something, just not the dihedral I want to restrain.

Thanks.

Josh

On Thu, September 8, 2005 11:13 pm, Joshua D. Moore wrote:
> When I use:
>
> freeEnergy on
> freeEnergyConfig {
>
> urestraint {
>
> dihe (C4E1,1,O1) (C4E1,1,C5) (C4E1,1,C6) (C4E1,1,O2) barr = 20
> ref = 180
>
> }
> }
>
> I get
>
> Info: *******************************
> FreeEnergy:
> FreeEnergy: Problem parsing input parameters
> FreeEnergy: Error: Invalid AtomID
> FreeEnergy: Read Until: (c4e1,1,o1) (c4e1,1,c5) (c4e1,1,c6) (c4e1,1,o2)
> barr = 20 ref = 180
>
> }
>
> FreeEnergy:
> FATAL ERROR: FreeEnergy: Fatal Parsing Error
>
>
> What I am trying to do is to restrain a single dihedral angle as
> indicated. Is there a better way to do this, and why isn't this working?
> From my .pdb file my segname is "C4E1", my residue # is "1", and my atom
> names are "O1,C5,C6,O2", which appears to be what the documentation calls
> for in the user's manual. However, it appears that I am not defining my
> AtomID properly.
>
> All I want is to restrain this single dihedral angle.
>
> Thanks for your help.
>
> --------------------------------------------------
> Joshua D. Moore
> Graduate Student
> North Carolina State University
> Department of Chemical and Biomolecular Engineering
> Box 7905 Centennial Campus
> Engineering Building I
> 911 Partners Way
> Raleigh, NC 27695-7905
> Phone: (919) 513-2051
> Fax: (919) 513-2470
> Email: jdmoore_at_unity.ncsu.edu
> --------------------------------------------------
>
>

--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
--------------------------------------------------

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