[gmx-users] Something about getting started

[DreamCatcher]

Dear gmx-users,
      I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol
simulation.But I don't even know how to start it.
      Is it necessary to start my simulation with a .pdb files?If so,What
should I do before this?I can make an pdb file for a chain of syndiotatic
polyvinyl-alcohols via Material Studio or some other packages,but the
residue cann't be recognize,so I have to modify some top files to correct
it.I just modify the .hdb and rtp files endeavor to make it.But it seems not
an easy work.
     the message the package sent to me is as follows,appreciate if somebody
can help me to handle this!
*** (this is an previous version.when i try to use pdb2gmx to get its .top
file,a fatal error reminds:
     "source code file : resall.c line:279 ()
       Fatal errors:
            in .rtp file at line :    "
     when I add the charge and chargegroupndx of the atoms,there comes a
similar error  ):
My attempt is as follows:
###  in rtp file
[ VAB ]
 [ atoms ]
  CB  opls_135
  HB1  opls_140
  HB2  opls_140
  HB3  opls_140
   CA  opls_158
  HA1  opls_140
   OH  opls_154
   HO  opls_155

 [ bonds ]
   CB  HB1
   CB  HB2
   CB  HB3
   CB   CA
   CA  HA1
   CA   OH
   OH   HO
   CA  +CB

[VA ]
 [ atoms ]
    CB  opls_136
   HB1  opls_140
   HB2  opls_140
    CA  opls_158
   HA1  opls_140
   OA  opls_154
  HOA  opls_155
   CG  opls_136
  HG1  opls_140
  HG2  opls_140
   CD  opls_158
   HD  opls_140
   OD  opls_154
  HOD  opls_155

 [ bonds ]
   CB    -CA
   CB   HB1
   CB   HB2
   CB    CA
   CA   HA1
   CA   OH
   OH   HO
   CA    CG
   CG   HG1
   CG   HG2
   CG   CD
   CD    HD
   CD   OD
   OD   HOD
   CD   +CB

[VAE]
 [ atoms ]
   CB  opls_136
   HB1  opls_140
   HB2  opls_140
    CA  opls_157
   HA1  opls_140
   HA2  opls_140
   OH  opls_154
   HO  opls_155

 [ bonds ]
   CB  -CD
   CB  HB1
   CB  HB2
   CB   CA
   CA  HA1
   CA  HA2
   CA   OH
   OH   HO

#### in .hdb file:
; H add type H i j k
VAB    3
3 4 HB  CB  CA  +CB
1 5 HA  CA  CB  +CB
1 2 HO  OH  CA  +CB
VA      6
2 6 HB  CB  CA  -CA
1 5 HA  CA  CB   CG
1 2 HOA OA  CA   CG
2 6 HG  CG  CA   CD
1 5 HD  CD  CG  +CB
1 1 HOD OD  CD  CG
VAE     3
2 6 HB  CB  CA  -CD
2 6 HA  CA  CB  +CB
1 2 HO  OH  CA  +CB
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