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: 10-Sep-04 16:24:09 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/volkman/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>MET SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =MET SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =ILE SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =CYS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =TRP SEQUence-element (terminate with END) =ASN SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =ASN SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =TRP SEQUence-element (terminate with END) =CYS SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =CYS SEQUence-element (terminate with END) =ARG SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =ILE SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =ASN SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =TRP SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =ILE SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =MET SEQUence-element (terminate with END) =PRO SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =MET SEQUence-element (terminate with END) =PHE SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =ILE SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =VAL SEQUence-element (terminate with END) =GLY SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =ASP SEQUence-element (terminate with END) =GLU SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =GLN SEQUence-element (terminate with END) =SER SEQUence-element (terminate with END) =THR SEQUence-element (terminate with END) =ILE SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) =LYS SEQUence-element (terminate with END) =HIS SEQUence-element (terminate with END) =LEU SEQUence-element (terminate with END) =ALA SEQUence-element (terminate with END) = end CHAIN> end SEGMENT>end SEGMNT: 124 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 1962(MAXA= 36000) NBOND= 1986(MAXB= 36000) NTHETA= 3608(MAXT= 36000) NGRP= 126(MAXGRP= 36000) NPHI= 3136(MAXP= 60000) NIMPHI= 1032(MAXIMP= 24000) NDON= 214(MAXPAD= 10000) NACC= 178(MAXPAD= 10000) NNB= 738(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 50 ) PATCH> reference=2=( resid 53 ) PATCH> end XPLOR: current counts (number in parenthesis is maximum) NATOM= 1960(MAXA= 36000) NBOND= 1984(MAXB= 36000) NTHETA= 3606(MAXT= 36000) NGRP= 128(MAXGRP= 36000) NPHI= 3136(MAXP= 60000) NIMPHI= 1032(MAXIMP= 24000) NDON= 212(MAXPAD= 10000) NACC= 178(MAXPAD= 10000) NNB= 738(MAXNB= 30000) X-PLOR> X-PLOR> X-PLOR>! turn peptide from trans to cis X-PLOR>patch CISP reference=nil=( resid 92 ) end XPLOR: current counts (number in parenthesis is maximum) NATOM= 1960(MAXA= 36000) NBOND= 1984(MAXB= 36000) NTHETA= 3606(MAXT= 36000) NGRP= 128(MAXGRP= 36000) NPHI= 3136(MAXP= 60000) NIMPHI= 1032(MAXIMP= 24000) NDON= 212(MAXPAD= 10000) NACC= 178(MAXPAD= 10000) NNB= 738(MAXNB= 30000) X-PLOR> X-PLOR> X-PLOR> X-PLOR>evaluate ( $par_nonbonded = "OPLSX" ) X-PLOR>parameter reset end X-PLOR> X-PLOR>parameter @TOPPAR:parallhdg5.3.pro end 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= 3972 current= 0 HEAP: maximum use= 894540 current use= 820272 X-PLOR: total CPU time= 0.4600 s X-PLOR: entry time at 16:24:09 10-Sep-04 X-PLOR: exit time at 16:24:09 10-Sep-04