VMD-L Mailing List

From: Marc Charendoff (mcharend_at_sbcglobal.net)
Date: Thu Feb 10 2011 - 15:40:14 CST

Hello all,

    I've got a question. I've run psfgen on a peptide twice with one psf file
generating cross terms, the other one with none. With my namd conf file
declaring par_all27_prot_na_carb.prm, only the psf file not specifying cross
terms runs. What are these cross terms? I'm thinking my psfing has not been
consistent. My file psf headers are:

PSF

       6 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS 2 patches were applied to the molecule.
 REMARKS topology helixb_ed_autopsf-temp.top
 REMARKS segment P1 { first PROP; last CTER; auto angles dihedrals }
 REMARKS patch PROP P1:1
 REMARKS patch CTER P1:15

.......and........

PSF CMAP (is this CMAP a clue?)

       6 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS 2 patches were applied to the molecule.
 REMARKS topology extnd3L4F_autopsf-temp.top
 REMARKS segment P1 { first PROP; last CTER; auto angles dihedrals }
 REMARKS patch PROP P1:1
 REMARKS patch CTER P1:15
 
...which gives me the extra "goodies".....

      13 !NCRTERM: cross-terms
      15 17 19 29 17 19 29 31
      29 31 33 46 31 33 46 48
      46 48 50 58 48 50 58 60
      58 60 62 75 60 62 75 77
      75 77 79 89 77 79 89 91
      89 91 93 99 91 93 99 101
      99 101 103 123 101 103 123 125
     123 125 127 147 125 127 147 149
     147 149 151 171 149 151 171 173
     171 173 175 193 173 175 193 195
     193 195 197 215 195 197 215 217
     215 217 219 237 217 219 237 239
     237 239 241 252 239 241 252 257