Xplor-NIH home Documentation |
Next: Example: A Polypeptide Chain Up: Generating the Molecular Structure Previous: Requirements
Example: A Polypeptide Chain
The following example file shows how to set up a polypeptide segment
(Tyr, Ala, Glu, Lys, Ile, Ala), assuming
that the topology and parameters have been previously read.
For completeness, the definitions of the patch residues
PEPT, PROP, NTER, and CTER have been included. Normally,
these patch residues are already defined in the topology
files.
topology PRESidue PEPT ADD BOND -C +N ADD ANGLE -CA -C +N ADD ANGLE -O -C +N ADD ANGLE -C +N +CA ADD ANGLE -C +N +H ADD DIHEdral -C +N +CA +C ADD DIHEdral -N -CA -C +N ADD DIHEdral -CA -C +N +CA ADD IMPRoper -C -CA +N -O {planar -C} ADD IMPRoper +N -C +CA +H {planar +N} END PRESidue PEPP ADD BOND -C +N ADD ANGLE -CA -C +N ADD ANGLE -O -C +N ADD ANGLE -C +N +CA ADD ANGLE -C +N +CD ADD DIHEdral -C +N +CA +C ADD DIHEdral -N -CA -C +N ADD DIHEdral -CA -C +N +CA ADD IMPRoper -C -CA +N -O {planar -C} ADD IMPRoper +N +CA +CD -C {planar +N} END PRESidue NTER GROUp ADD ATOM +HT1 TYPE=HC CHARge=0.35 END ADD ATOM +HT2 TYPE=HC CHARge=0.35 END MODIfy ATOM +N TYPE=NH3 CHARge=-0.30 END ADD ATOM +HT3 TYPE=HC CHARge=0.35 END DELETE ATOM +H END MODIfy ATOM +CA CHARge=0.25 END ADD BOND +HT1 +N ADD BOND +HT2 +N ADD BOND +HT3 +N ADD ANGLe +HT1 +N +HT2 ADD ANGLe +HT2 +N +HT3 ADD ANGLe +HT2 +N +CA ADD ANGLe +HT1 +N +HT3 ADD ANGLe +HT1 +N +CA ADD ANGLe +HT3 +N +CA ADD DIHEdral +HT2 +N +CA +C ADD DIHEdral +HT1 +N +CA +C ADD DIHEdral +HT3 +N +CA +C ADD DONOr +HT1 +N ADD DONOr +HT2 +N ADD DONOr +HT3 +N END PRESidue PROP GROUp ADD ATOM +HT1 TYPE=HC CHARge= 0.35 END ADD ATOM +HT2 TYPE=HC CHARge= 0.35 END MODIfy ATOM +N TYPE=NH3 CHARge=-0.20 END MODIfy ATOM +CD CHARge= 0.25 END MODIfy ATOM +CA CHARge= 0.25 END ADD BOND +HT1 +N ADD BOND +HT2 +N ADD ANGLe +HT1 +N +HT2 ADD ANGLe +HT2 +N +CA ADD ANGLe +HT1 +N +CD ADD ANGLe +HT1 +N +CA ADD ANGLe +CD +N +HT2 ADD DIHEdral +HT2 +N +CA +C ADD DIHEdral +HT1 +N +CA +C ADD DONOr +HT1 +N ADD DONOr +HT2 +N END PRESidue CTER GROUp MODIfy ATOM -C CHARge= 0.14 END ADD ATOM -OT1 TYPE=OC CHARge=-0.57 END ADD ATOM -OT2 TYPE=OC CHARge=-0.57 END DELETE ATOM -O END ADD BOND -C -OT1 ADD BOND -C -OT2 ADD ANGLe -CA -C -OT1 ADD ANGLe -CA -C -OT2 ADD ANGLe -OT1 -C -OT2 ADD DIHEdral -N -CA -C -OT2 ADD IMPRoper -C -CA -OT2 -OT1 ADD ACCEptor -OT1 -C ADD ACCEptor -OT2 -C END end segment name="PROT" chain link pept head - * tail + * end first prop tail + pro end ! special n-ter for PRO first nter tail + * end last cter head - * end sequence TYR ALA GLU LYS ILE ALA end end endThe information about the patch residues is normally included in the topology file. The information about the peptide linkages is also included in the “toph19.pep" file in the “toppar" directory. Wildcards allow one to use the same patch residues (“PEPT") for all combinations of amino acids. The only exception is Pro, which needs a special N-terminal patch. The residues are numbered consecutively, starting with 1. To use a particular numbering for residues, one should use the COOR option to read the sequence from the coordinate file.
Xplor-NIH 2024-09-13