[gmx-users] building Topologies

[Jessé Nóbrega]

Hi gmx-users,

I have trying build topologies for PVC polymer in opls/aa forcefield. I read the chapter 5 and modified the files ffoplsaa.rtp, ffoplsaa.hdb, ffoplsaa-n.tdb, ffoplsaa-c.tdb, but not successful.
Below, you can see the blocks that built. The parameters for the residue may seem confusing, but I  am trying to understand how to build these blocks and then create new parameters for the residue.

rtp file:

[ VIN ]
 [ atoms ]
    C1    opls_136    -0.120    1
   H11   opls_140     0.060    1
   H12   opls_140     0.060    1
    C2    opls_001     0.500    2
    Cl     opls_151    -0.200    2
   H21   opls_153     0.103    2
 [ bonds ]
   C1      H11
   C1      H12
   C1       C2
   C2       Cl
   C2      H21
   C2      +C1

hdb file

VIN     2
            2       6       H1       C1      C2     +C1
            1       6       H2       C2      C1     -C2

-c.tdb file:

[ VIN ]
 [ replace ]
    C1      opls_135        12.011  -0.18
 [ add ]
    3        4      H1      C1      C2
            opls_140       1.008   0.06
[ delete ]
   H21

-n.tdb file:

[ VIN ]
[ replace ]
C               opls_152        12.011 -0.006
[ add ]
2      4        H       C2      C1
       opls_153        1.00800  0.103
[ delete ]
  H21

By using the pdb2gmx following error occurs:

Opening library file ffoplsaa.rtp
Opening library file /usr/local/gromacs332/share/gromacs/top/aminoacids.dat
Reading PVC_32_mon_1_cd_gromos.pdb...
WARNING: all CONECT records are ignored
Read 194 atoms
Opening library file /usr/local/gromacs332/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 32 residues with 194 atoms

  chain  #res #atoms
  1 ' '    32    194

All occupancies are one
Opening library file /usr/local/gromacs332/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
Residue 57
Sorting it all out...
Opening library file ffoplsaa.hdb
Opening library file ffoplsaa-n.tdb

-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 3.3.2
Source code file: h_db.c, line: 95

Fatal error:
Error in hdb file ffoplsaa-n.tdb:
Wrong number of control atoms (2 iso 3) on line:
2      4        H       C2      C1

Why this error occur?

Excuse me my English, I am a beginner in the language. 

Thank you very much



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