remarks   file  geomanal/geomanal.inp
remarks   Analyze geometry and nonbonded contacts 

                                                     {*Read structure file.*}
{===>} structure @../generate/generate.psf end  

                                                        {*Read coordinates.*}
{===>} coordinates @../xtalrefine/slowcool.pdb 

{===>} vector ident (store9) ( not hydrogen )       
                                             {*This selects all atoms to be*}
                                             {*analyzed.  Change it        *}
                                             {*to analyze portions,        *}
                                             {*e.g., ( segid "A" ).        *}
                 

parameter 
   {===>} @TOPPAR:parhcsdx.pro          {*Read empirical energy parameters.*}
end


xrefine                        {*Unit cell parameters and crystal symmetry.*} 

{===>}   a=61.76 b=40.73 c=26.74 alpha=90.0 beta=90.0 gamma=90.0  
                                             
{===>}   symmetry=(x,y,z)                          
         symmetry=(-x+1/2,-y,z+1/2)                
         symmetry=(-x,y+1/2,-z+1/2)                
         symmetry=(x+1/2,-y+1/2,-z)
end      


           {*Deviations of the geometry*}
           {*==========================*}

constraints interaction                       {*This command selects the   *}
    ( store9 ) ( store9 )                     {*atoms to be                *}
end                                           {*considered in the following*}
                                              {*analysis.                  *}

print threshold=0.06 bonds                  {*Lists bonds deviating more   *}
                                            {*than 0.06 A from ideality.   *}

print threshold=10.0 angles                {*Lists angles deviating more   *}
                                           {*than 10 degrees from ideality.*}

print threshold=90.0 dihedrals             {*Lists dihedrals deviating more*}
                                           {*than 90 degrees from ideality.*}

print threshold=20.0 impropers             {*Lists impropers deviating more*}
                                           {*than 20 degrees from ideality.*}

          {*bad? contacts and nonbonded energy*}
          {*==================================*}
flags exclude * include vdw elec pvdw pele end
energy end

          {*crystal packing contacts*}
          {*========================*}
flags exclude * include pvdw end


distance from=( not hydrogen ) to=( not hydrogen ) cutoff=4.0 end
 
stop