Merge pull request #787 from haddocking/topoaa

Solves issue #785 about unstable energies when changing the param file

src/haddock/cns/toppar/hemes-allhdg.top

@@ -1,7 +1,7 @@
 remark file topallhdg.hemes
 
 set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result)
-set message=off echo off=end
+set message=off echo=off end
 
 autogenerate
   angles=true

src/haddock/modules/topology/topoaa/cns/build-missing.cns

@@ -74,9 +74,11 @@ if ( $tobuild > 0 ) then
 
         end loop bndto 
 
-        do (x=x+2*random(1.0)-1) (store9)
-        do (y=y+2*random(1.0)-1) (store9)
-        do (z=z+2*random(1.0)-1) (store9)
+        for $id in id (store9) loop radis
+            do (x=x+2*random(1.0)-1) (id $id)
+            do (y=y+2*random(1.0)-1) (id $id)
+            do (z=z+2*random(1.0)-1) (id $id)
+        end loop radis
 
         {- start parameter for the side chain building -}
         parameter
@@ -135,7 +137,7 @@ if ( $tobuild > 0 ) then
             nprint=$nstep
             cmremove=false
         end
-  
+
         parameter
             nbonds
                 rcon=2. nbxmod=-3 repel=0.75
@@ -170,13 +172,11 @@ if ( $tobuild > 0 ) then
 
         flags exclude * include bond angl impr dihe vdw elec end
 
+        minimize powell nstep=500 nprint=50 end
+
         {- return masses to something sensible -}
         do (mass=refy) (store9)
 
-        do (vx=maxwell($bath)) (store9)
-        do (vy=maxwell($bath)) (store9)
-        do (vz=maxwell($bath)) (store9)
-
         dynamics cartesian
             nstep=$nstep
             timestep=$timestep

src/haddock/modules/topology/topoaa/cns/generate-topology.cns

@@ -712,10 +712,7 @@ end if
 
 delete selection=( &atom_delete ) end
 
-inline @MODULE:build-missing.cns
-
 !check for histidine protonation state if auto mode on
-!but only for the first model
 if ($autohis = true) then
     inline @MODULE:auto-his.cns
 end if
@@ -804,9 +801,6 @@ buffer message
 end
 buffer message reset end
 
-!do (segid = "    ") (all)
-!do (segid = $prot_segid_1) (all)
-
 write structure output=$output_psf_filename end
 write coordinates format=pdbo output=$output_pdb_filename end