[gmx-users] Polyethylene Surface generation

[Yash Gandhi]

Hi,
A few days ago I had posted a request regarding help with Polyethylene
surface generation. I had earlier taken help of an older thread to create a gmx
file for PE<http://www.google.com/url?sa=t&source=web&cd=2&ved=0CB4QFjAB&url=http%3A%2F%2Fwww.mail-archive.com%2Fgmx-users%40gromacs.org%2Fmsg19681.html&ei=j5ypTKHdAcyHcYPrkN8N&usg=AFQjCNEkAowW5JCRzjdf8pZyHNj0shEcSg&sig2=5dYMLHgV6B99F848iAPOEQ>.
I also did the modifications in rtp and hdb files as mentioned in the link.
After a few thoughts I tried to create a pdb file using some logic. It's as
follows:

HETATM    1  C1   EtB        1      -4.243   0.027  -1.420
HETATM    2  C2   EtB      1      -2.975  -0.719  -0.982
HETATM    3  C1   Eth      2      -1.840   0.252  -0.620
HETATM    4  C2   Eth      2      -0.566  -0.487  -0.180
HETATM    5  C1   Eth      3       0.567   0.487   0.181
HETATM    6  C2   Eth      3       1.841  -0.252   0.621
HETATM    7  C1   EtE      4       2.976   0.719   0.983
HETATM    8  C2   EtE      4       4.244  -0.026   1.420
HETATM    9  H11  EtB      1      -5.058  -0.688  -1.680
HETATM   10  H12  EtB      1      -4.048   0.659  -2.317
HETATM   11  H13  EtB      1      -4.620   0.690  -0.609
HETATM   12  H21  EtB      1      -2.642  -1.393  -1.807
HETATM   13  H22  EtB      1      -3.213  -1.362  -0.102
HETATM   14  H11  Eth      2      -2.179   0.926   0.202
HETATM   15  H12  Eth      2      -1.609   0.895  -1.503
HETATM   16  H21  Eth      2      -0.227  -1.161  -1.003
HETATM   17  H22  Eth      2      -0.797  -1.130   0.702
HETATM   18  H11  Eth      3       0.228   1.161   1.003
HETATM   19  H12  Eth      3       0.798   1.129  -0.702
HETATM   20  H21  Eth      3       2.180  -0.926  -0.202
HETATM   21  H22  Eth      3       1.610  -0.895   1.504
HETATM   22  H11  EtE      4       2.643   1.393   1.807
HETATM   23  H12  EtE      4       3.213   1.362   0.102
HETATM   24  H21  EtE      4       5.059   0.688   1.679
HETATM   25  H22  EtE      4       4.621  -0.690   0.608
HETATM   26  H23  EtE      4       4.050  -0.658   2.317
CONECT    1    2
CONECT    2    1    3
CONECT    3    2    4
CONECT    4    3
END

after running pdb2gmx command and taking OPLSAA Force field with the
additional residues as mentioned in the link, I am getting the same error
always and I am not able to get the reason why
*
Fatal error:
Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
             while sorting atoms*

Please help me urgently as I am not able to know why is the EtOH residue
being used.

Thanking you
-- 
Yash Gandhi,
4th Year, BE (Hons) Chemical,
Birla Institute of Technology & Science, Pilani, India
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