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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