From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jun 27 2007 - 01:42:51 CDT
Hi Jerome,
Before I send you the files, you should know that I am also also using some
standard NAMD harmonic constraints on parts of the protein backbone. I am
hoping that should be compatible with ABF constraints (which are applied on
a different set of atoms ) ?
-Maria
On 6/26/07, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
>
> Hi Maria,
> Can you send me (off-list) the necessary files for me to reproduce the
> problem?
> Thanks,
> Jerome
>
> On 6/26/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
> > Hi,
> >
> > I am trying to use abf to constrain dihedrals using the coordinate dummy
> > feature as suggested by Jerome Henin earlier.
> >
> > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6083.html
> >
> > However, after a few steps, NAMD crashes giving me an error "force not a
> > vector". I also tried the file forces.tcl in the following thread, but
> that
> > does not help.
> >
> > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3043.html
> >
> > I am using a total of 48 dihedral restraints. Here is the core of my abf
> > script:
> > ###################
> > abf coordinate dummy
> > abf restraintList {
> > d1 {dihe {PRO1 195 C} {PRO1 196 N} {PRO1 196 CA} {PRO1
> 196 C}
> > 30 -60}
> > d2 {dihe {PRO1 196 N} {PRO1 196 CA} {PRO1 196 C} {PRO1
> 197 N}
> > 30 -45}
> > d3 {dihe {PRO1 196 C} {PRO1 197 N} {PRO1 197 CA} {PRO1
> 197 C}
> > 30 -60}
> > d4 {dihe {PRO1 197 N} {PRO1 197 CA} {PRO1 197 C} {PRO1
> 198 N}
> > 30 -45}
> > d5 {dihe {PRO1 197 C} {PRO1 198 N} {PRO1 198 CA} {PRO1
> 198 C}
> > 30 -60}
> > ..
> > ..
> > }
> > ###################
> >
> > Thank you
> >
> > -Maria
> >
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
>
-- Maria G. Technical University of Denmark Copenhagen
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