XPLOR-NIH version 2.0.6 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: on: linux/intel at: 8-Mar-05 21:02:38 X-PLOR>remarks changed Tue Sep 2 09:48:07 CDT 2003 X-PLOR>remarks by jfd to include a fes residue X-PLOR> X-PLOR>!@generate_tmoc.inp X-PLOR> X-PLOR>topology reset end X-PLOR>structure reset end XPLOR: current counts (number in parenthesis is maximum) NATOM= 0(MAXA= 36000) NBOND= 0(MAXB= 36000) NTHETA= 0(MAXT= 36000) NGRP= 0(MAXGRP= 36000) NPHI= 0(MAXP= 60000) NIMPHI= 0(MAXIMP= 24000) NDON= 0(MAXPAD= 10000) NACC= 0(MAXPAD= 10000) NNB= 0(MAXNB= 30000) X-PLOR> X-PLOR>topology RTFRDR>{===>} @TOPPAR:topallhdg5.3.pro ASSFIL: file /u/lytle/waterrefine/toppar/topallhdg5.3.pro opened. RTFRDR>remark file topallhdg.pro version 5.3 date 23-Sept-02 RTFRDR>remark for file parallhdg.pro version 5.3 date 13-Feb-02 or later RTFRDR>remark Geometric energy function parameters for distance geometry and RTFRDR>remark simulated annealing. RTFRDR>remark Author: Michael Nilges, EMBL Heidelberg; Institut Pasteur, Paris RTFRDR>remark This file contains modifications from M. Williams, UCL London RTFRDR>remark Last modification 16-Sept-02 RTFRDR> RTFRDR>set echo off message off end RTFRDR>end X-PLOR> X-PLOR>! no chain id. X-PLOR>segment name=" " SEGMENT> chain CHAIN> @TOPPAR:topallhdg5.3.pep CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> @1xxx.seq SEQUENCE>ASP SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =ASN SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =ARG SEQUence-element (terminate with END) =CYS SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =CYS SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =ARG SEQUence-element (terminate with END) =TYR SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =ILE SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =ASN SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =ARG SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =ARG SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =TYR SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =ARG SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =MET SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =TYR SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) = end CHAIN> end SEGMENT> chain CHAIN> sequence SEQUENCE> ZIN SEQUence-element (terminate with END) = end CHAIN> end SEGMENT>end SEGMNT: 68 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 1046(MAXA= 36000) NBOND= 1057(MAXB= 36000) NTHETA= 1903(MAXT= 36000) NGRP= 70(MAXGRP= 36000) NPHI= 1607(MAXP= 60000) NIMPHI= 559(MAXIMP= 24000) NDON= 131(MAXPAD= 10000) NACC= 102(MAXPAD= 10000) NNB= 258(MAXNB= 30000) X-PLOR> X-PLOR>! removes the hydrogen on the cys-en X-PLOR>! and changes the atom type from SH1E to S. X-PLOR>!patch DISN reference=1=( resid 18 ) X-PLOR>! reference=2=( resid 21 ) X-PLOR>! end X-PLOR> X-PLOR>! turn doubly protonated his to singly protonated histidine (HD1) X-PLOR>!patch HISD reference=nil=( resid 34 ) X-PLOR>! reference=nil=( resid 40 ) X-PLOR>! end X-PLOR> X-PLOR>patch ZINC PATCH> reference=1=( resid 18 ) PATCH> reference=2=( resid 21 ) PATCH> reference=3=( resid 34 ) PATCH> reference=4=( resid 40 ) PATCH> reference=5=( resid 68 ) PATCH>end XPLOR: current counts (number in parenthesis is maximum) NATOM= 1042(MAXA= 36000) NBOND= 1057(MAXB= 36000) NTHETA= 1909(MAXT= 36000) NGRP= 70(MAXGRP= 36000) NPHI= 1607(MAXP= 60000) NIMPHI= 563(MAXIMP= 24000) NDON= 127(MAXPAD= 10000) NACC= 102(MAXPAD= 10000) NNB= 258(MAXNB= 30000) X-PLOR> X-PLOR>! turn peptide from trans to cis X-PLOR>!patch CISP reference=nil=( resid 80 ) end X-PLOR> X-PLOR> X-PLOR>evaluate ( $par_nonbonded = "OPLSX" ) X-PLOR>parameter reset end X-PLOR> X-PLOR>parameter @TOPPAR:parallhdg5.3.pro PARRDR>! JFD adds FES complex parameters from Milo Westler's calculations PARRDR>! and standard topology. PARRDR> PARRDR>remark file protein-allhdg-ucl.param version UCL date 07-JUL-01 PARRDR>remark for file protein-allhdg-ucl.top version UCL date 14-MAR-00 PARRDR>remark for file protein-allhdg-dih-ucl.top version UCL date 07-JUL-01 PARRDR>remark Geometric energy function parameters for distance geometry and PARRDR>remark simulated annealing. PARRDR>remark Original author: Michael Nilges, EMBL Heidelberg PARRDR>remark Modifications: Mark A. Williams, UCL London PARRDR> PARRDR>set echo off message off end CSTACK: size= 40000 used= 2138 current= 0 HEAP: maximum use= 890868 current use= 820272 X-PLOR: total CPU time= 0.2400 s X-PLOR: entry time at 21:02:38 8-Mar-05 X-PLOR: exit time at 21:02:38 8-Mar-05