remarks file toppar/protein_break.top
remarks   patches to remove peptide linkages

! Paul Adams 28th June 1999
! Yale University

set echo=false end

checkversion 1.2

PRESidue DPEP { delete PEPTide bond link, for all 
                amino acids ...*(-)     (+)*...
                                 \ PEPT /

                except the  *(-) - (+)PRO link }

 DELEte BOND -C +N 

 DELEte ANGLE -CA -C +N
 DELEte ANGLE -O  -C +N
 DELEte ANGLE -C  +N +CA
 DELEte ANGLE -C  +N +H

 DELEte DIHEdral  -C +N +CA +C
 DELEte DIHEdral  -N -CA -C +N
 DELEte DIHEdral  -CA -C +N +CA

 DELEte IMPRoper  -C -CA +N -O
 DELEte IMPRoper  +N -C +CA +H

END {DPEP}

!----------------------------------------------------------------------

PRESidue DPPP  { for  ...*(-) - (+)PRO  link deletion
                 same as DPEP except replacement H by CD
                 and improper +N +CA +CD -C }

 DELEte BOND -C +N 

 DELEte ANGLE -CA -C +N
 DELEte ANGLE -O  -C +N
 DELEte ANGLE -C  +N +CA
 DELEte ANGLE -C  +N +CD

 DELEte DIHEdral  -C +N +CA +C
 DELEte DIHEdral  -N -CA -C +N
 DELEte DIHEdral  -CA -C +N +CA

 DELEte IMPRoper  -C -CA +N -O
 DELEte IMPRoper  +N +CA +CD -C

END {DPPP}

!------------------------------------------------------------------

set echo=true end