W dniu poniedziałek, 1 lipca 2013 15:09:12 UTC+1 użytkownik Christoph
Junghans napisał:
>
> 2013/7/1 <[email protected] <javascript:>>:
> > I am trying to run IBI for angles. I calculated 88 distributions for
> angles
> > (its a protein made of 90 beads) using csg_boltzmann.
> >
> > My question: shall I refine and smooth those ditributions?
> >
> > In my xml:
> >
> > <bonded>
> > <name>angle</name>
> > <min>1</min>
> > <max>3</max>
> > <step>0.05</step>
> > <inverse>
> > <target>angle.dist1</target>
> > <gromacs>
> > <table>table_a1.xvg</table>
> > </gromacs>
> > </inverse>
> > </bonded>
> >
> > How can I add the remaining angles so votca will know which angle
> > corresponds to which x y z atoms?
> >
> > Would that be
> >
> > <bonded>
> > <name>angle</name>
> > <min>1</min>
> > <max>3</max>
> > <step>0.05</step>
> > <inverse>
> > <target>angle.dist1</target>
> > <gromacs>
> > <table>table_a1.xvg</table>
> > </gromacs>
> > </inverse>
> > </bonded>
> > <bonded>
> > <name>angle</name>
> > <min>1</min>
> > <max>3</max>
> > <step>0.05</step>
> > <inverse>
> > <target>angle.dist2</target>
> > <gromacs>
> > <table>table_a2.xvg</table>
> > </gromacs>
> > </inverse>
> > </bonded>
> > etc?
> >
> > Or am I missing somethin and I should provide with one distribution
> > corresponding to all angles? Please, advise.
> You will have use different names for the different angles, something
> like angle1, ..., angle9 or angle_A_B_C ,..., angle_X_Y_Z.
> Remember that the names in the settings xml file and the mapping file
> have to be the same.
>
> Christoph
>
Thank you. So in settings file for angle names: angle1, angle2 etc the
mapping should be:
<cg_bonded>
<angle>
<name>angle1</name>
<beads>
1MET 2SER 3VAL
* </beads>*
<angle>
<name>angle2</name>
<beads>
1GLY 2SER 3ARG
* </beads>*
Am I correct?
How csg_inverse know the name of the mapping file? It is not specified in
the input of csg_inverse.
Steven
>
> > Steven
> >
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> >
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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