unres paper list update

[django_unres.git] / files / pbs_md_new.csh

diff --git a/files/pbs_md_new.csh b/files/pbs_md_new.csh
index 6a678a8..57900e0 100755 (executable)
--- a/files/pbs_md_new.csh
+++ b/files/pbs_md_new.csh
@@ -12,7 +12,7 @@ setenv THETPARPDB $DD/thetaml_ext.5parm
 setenv ROTPARPDB $DD/scgauss_ext.parm
 setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
 setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
-setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv TORDPAR $DD/torsion_double_631Gdp_old_ext.parm
 setenv ELEPAR $DD/electr_631Gdp_ext.parm
 setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
 setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
@@ -46,13 +46,25 @@ if ( -f "file_MD000.pdb" ) then
  mkdir tmp
  /users2/local/pymol_1.6/pymol -c ../files/movie.pml
  ffmpeg2theora tmp/aa%4d.png -o md.ogv
- rm -rf tmp
+ if ( `grep -c pdbstart file.inp` ) then
+  /users2/local/pymol_1.6/pymol -c ../files/overlap.pml
+  ../files/fluct_plot.py intra_fit.pdb > fluctuations.txt
+  /users2/local/pymol_1.6/pymol -c -r ../files/fluct.py
+  rm -f intra_fit.pdb
+ endif
+ rm -rf tmp 
 else
  /users2/czarek/UNRES/git3_tmp/build/bin/xdrf2pdb-mult one file.seq file_MD000.cx
  mkdir tmp
  /users2/local/pymol_1.6/pymol -c ../files/movie.pml
  ffmpeg2theora tmp/aa%4d.png -o md.ogv
- rm -rf tmp file_MD000.pdb
+ if ( `grep -c pdbstart file.inp` ) then 
+  /users2/local/pymol_1.6/pymol -c ../files/overlap.pml
+  ../files/fluct_plot.py intra_fit.pdb > fluctuations.txt
+  /users2/local/pymol_1.6/pymol -c -r ../files/fluct.py
+  rm -f intra_fit.pdb
+ endif
+ rm -rf tmp file_MD000.pdb 
 endif
 
 touch finished