From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 22 2015 - 02:55:09 CST
It seems that the center for colvar "d" is lacking for the intended
purpose. If so, which is the most appropriate for "?".
colvars d RMSD ORIENT
centers ?.? 0.0 (1, 0, 0, 0) # centered around zero displ, zero RMSD and
no rotation
thanks
fp
On Wed, Jan 21, 2015 at 8:01 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> I forgot to mention that all three colvars include the index of all atoms
> of the active center and the index of the six CA atoms at the protein
> backbone to which the active center is bound. Does that create problems
> with "centers" The active center is at one chain only of the four chains
> of the enzyme.
>
> fp
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Wed, Jan 21, 2015 at 7:45 PM
> Subject: Local minima on minimiztion with colvars
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Hi:
> I am at a system of a multichain enzyme with a bimetallic active center
> bound through covalent carbon-carbon bonds. Amber parm10 data, parm7 file.
> I rebuilt the system by removing all crystallization water and letting leap
> to set the H-atoms, which removed some hard ckashes. The only warnings from
> leap where about some short interatomic distances (1A the shortest)
>
> Minimization with distance-rmsd-orientaion colvars. I got the impression
> that minimization brings a portion of the active center (an acetate
> bridging the two metals) into local minima, with some twisting. My question
> is, could my colvar input be modified from run to run so that the issue of
> local minima is overcome?
>
> I should also point out that the minimization goes on if the harmonic only
> comprises rmsd and orientaion colvars. If I include the distance colvars
> "d", it crashes with "colvars: Error: in parsing "centers".
>
> Following is the colvar input
>
> # collective variable config file for "rmsd" and "orient" variable
> # using group
>
>
>
> colvar {
> name d
>
> width 0.2
>
> distance {
> group1 {
>
> atomNumbers 1628 2059...etc
>
> centerReference # use relative coordinates
> rotateReference # (translated and rotated frame of
> reference)
> refPositionsGroup { # Define frame of reference base on
> separate atom group
> atomsFile PROT_BOX_refB.pdb # from separate file
> atomsCol B
> }
> refPositionsFile PROT_BOX_refB.pdb # initial coordinates for
> reference group
> }
> group2 {
> dummyAtom (6.0, -1.0, -0.2) # fixed position
> }
> }
> }
>
>
> colvar {
> name RMSD # needed to identify the variable
>
>
> width 0.3
> rmsd {
> atoms {
> #atomNumbers 7893 7901 7902 7909 7910 7911 7915 7922 7930 7931
> 7938 7939 7940 7950 7951 7952 7955 7961 7962
> # C2 O2 C5 O3 O4 C9 N1 C14 O6 C18 OE1
> OE2 CB NE2 FE1 O7 FE O OXT
> atomNumbers 1628 2059 etc
> }
>
> refPositionsFile PROT_BOX.pdb
> }
> }
>
>
>
> colvar {
> name ORIENT
>
> width 0.1
>
> orientation {
> atoms {
>
> atomNumbers 1628 2059 etc
> }
>
> refPositionsFile PROT_BOX.pdb
> }
> }
>
>
>
>
> harmonic { # define a moving harmonic restraint
>
> colvars RMSD ORIENT
>
> centers 0.0 (1, 0, 0, 0) # centered around zero RMSD and no rotation
>
> forceConstant 30.0 # unit is kcal/mol/[width]^2
> # where the width parameter is adapted to the dimensions of each colvar
> }
>
>
>
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:34 CST