[gmx-users] Polyethylene

[Zuzana Benkova]

Dear GMX users,
I want to prepare .gro and topology files starting from the .pdb file  
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.  
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as  
follows

[ Eth ]
  [ atoms ]
    C1    opls_136    -0.120    1
    H11   opls_140     0.060    1
    H12   opls_140     0.060    1
    C2    opls_136    -0.120    2
    H21   opls_140     0.060    2
    H22   opls_140     0.060    2
  [ bonds ]
    C1    H11
    C1    H12
    C1    C2
    C2    H21
    C2    H22
    C2    +C1
  In ffoplsaa.hdb I defined it as

Eth     2
2       6       H1       C1      C2     +C1
2       6       H2       C2      C1     -C2

At this point I have to note that the presence of the last control  
atoms in this file has not influenced the process.
In ffoplsaa-n.tdb file I have added

[ Eth ]
[ replace ]
C2      opls_135        12.011   -0.18
[ add ]
3        4      H2      C2      C1
          opls_140       1.008   0.06
[ delete ]
H21
H22

and in ffoplsaa-c.tdb file I have added

[ Eth ]
[ replace ]
C1      opls_135        12.011  -0.18
[ add ]
3        4      H1      C1      C2
          opls_140       1.008   0.06
[ delete ]
H11
H12

After using pdb2gmx -f input.pdb I have obtained following message

Opening library file ffoplsaa.rtp
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat
Reading hexane.pdb...
Read 6 atoms
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/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 3 residues with 6 atoms
   chain  #res #atoms
   1 ' '     3      6
All occupancies are one
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
Residue 59
Sorting it all out...
Opening library file ffoplsaa.hdb
Error in hdb file: nah = 41
line = ''
Opening library file ffoplsaa-n.tdb
Opening library file ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (6 atoms, 3 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms....
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
N-terminus: Eth
C-terminus: Eth
Segmentation fault

Could you specify what means Error in hdb file: nah = 41
line = '' and what is the problem with segmentation.

My input structure in .pdb file is as follows

ATOM      1  C1  Eth     1       1.000   1.540   0.000
ATOM      2  C2  Eth     1       2.456   2.041   0.000
ATOM      3  C1  Eth     2       2.456   3.581   0.000
ATOM      4  C2  Eth     2       3.912   4.083   0.000
ATOM      5  C1  Eth     3       3.912   5.623   0.000
ATOM      6  C2  Eth     3       5.368   6.124   0.000
END

Thank you for help in advance
Best regards
Zuzana