Hi,<br>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 <a href="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">gmx file for PE</a>. 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:<br>
<br>HETATM 1 C1 EtB 1 -4.243 0.027 -1.420
<br>HETATM 2 C2 EtB 1 -2.975 -0.719 -0.982
<br>HETATM 3 C1 Eth 2 -1.840 0.252 -0.620
<br>HETATM 4 C2 Eth 2 -0.566 -0.487 -0.180
<br>HETATM 5 C1 Eth 3 0.567 0.487 0.181
<br>HETATM 6 C2 Eth 3 1.841 -0.252 0.621
<br>HETATM 7 C1 EtE 4 2.976 0.719 0.983
<br>HETATM 8 C2 EtE 4 4.244 -0.026 1.420
<br>HETATM 9 H11 EtB 1 -5.058 -0.688 -1.680
<br>HETATM 10 H12 EtB 1 -4.048 0.659 -2.317
<br>HETATM 11 H13 EtB 1 -4.620 0.690 -0.609
<br>HETATM 12 H21 EtB 1 -2.642 -1.393 -1.807
<br>HETATM 13 H22 EtB 1 -3.213 -1.362 -0.102
<br>HETATM 14 H11 Eth 2 -2.179 0.926 0.202
<br>HETATM 15 H12 Eth 2 -1.609 0.895 -1.503
<br>HETATM 16 H21 Eth 2 -0.227 -1.161 -1.003
<br>HETATM 17 H22 Eth 2 -0.797 -1.130 0.702
<br>HETATM 18 H11 Eth 3 0.228 1.161 1.003
<br>HETATM 19 H12 Eth 3 0.798 1.129 -0.702
<br>HETATM 20 H21 Eth 3 2.180 -0.926 -0.202
<br>HETATM 21 H22 Eth 3 1.610 -0.895 1.504
<br>HETATM 22 H11 EtE 4 2.643 1.393 1.807
<br>HETATM 23 H12 EtE 4 3.213 1.362 0.102
<br>HETATM 24 H21 EtE 4 5.059 0.688 1.679
<br>HETATM 25 H22 EtE 4 4.621 -0.690 0.608
<br>HETATM 26 H23 EtE 4 4.050 -0.658 2.317
<br>CONECT 1 2
<br>CONECT 2 1 3
<br>CONECT 3 2 4
<br>CONECT 4 3
<br>END<br><br>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<br><i><br>Fatal error:<br>
Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms<br> while sorting atoms</i><br><br>Please help me urgently as I am not able to know why is the EtOH residue being used.<br><br clear="all">Thanking you<br>
-- <br>Yash Gandhi,<br>4th Year, BE (Hons) Chemical,<br>Birla Institute of Technology & Science, Pilani, India<br><br>