Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues need atom numbering..Hdb file was not helpful either because I think I need to have a structure file with only coordinates of carbon atoms (hdb adds H ). ...That coordinate file I dont know how to get.
I tried x2top command to generate top file and I got LINCS error. I followd the tips you had given before on how to diagnose a crashing system and thats why I suspect top file is not produced properly when I have no atom numbering in coordinate file. Now I am following your suggestion to use genconf command to build up my polymer. The distance between C -C atoms in ethylene is 1.52 A. So I considred 0.76 A as distance from each side, and 1.52+ 2*0.76=3.04 A as box size. In the command line below I entered 0.304 to convert to nm. Please see below: Initsial pdb file: HETATM 1 C1 EthB 1 2.739 2.554 -0.012 0.00 -0.39 C HETATM 2 H11 EthB 1 2.736 3.644 -0.012 0.00 0.13 H HETATM 3 H12 EthB 1 2.190 2.217 -0.893 0.00 0.13 H HETATM 4 H13 EthB 1 2.190 2.217 0.868 0.00 0.13 H HETATM 5 C2 EthB 1 4.155 1.993 -0.012 0.00 -0.26 C HETATM 6 H21 EthB 1 4.696 2.362 -0.887 0.00 0.13 H HETATM 7 H22 EthB 1 4.696 2.362 0.862 0.00 0.13 H END editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 0.304 0.304 -angles 90 90 90 -d 0.076 7 1EthB C1 1 0.141 0.166 0.164 1EthB H11 2 0.141 0.275 0.164 1EthB H12 3 0.086 0.132 0.076 1EthB H13 4 0.086 0.132 0.252 1EthB C2 5 0.282 0.110 0.164 1EthB H21 6 0.337 0.147 0.077 1EthB H22 7 0.337 0.147 0.251 0.40260 0.31710 0.32810 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 genconf -f PEmonomer.gro -sort -o PEsort -nbox 5 I use -sort to align the molecule with X coordinate and want to replicate 5 boxes. Am I using correctly the -sort option? What I get is: 8875 1EthB C1 1 0.086 0.132 0.252 0.0000 0.0000 0.0000 1EthB H11 2 0.282 0.110 0.164 0.0000 0.0000 0.0000 1EthB H12 3 0.337 0.147 0.077 0.0000 0.0000 0.0000 1EthB H13 4 0.086 0.132 0.404 0.0000 0.0000 0.0000 1EthB C2 5 0.086 0.132 0.580 0.0000 0.0000 0.0000 1EthB H21 6 0.282 0.110 0.492 0.0000 0.0000 0.0000 1EthB H22 7 0.086 0.132 1.236 0.0000 0.0000 0.0000 2EthB C1 8 0.282 0.110 1.148 0.0000 0.0000 0.0000 2EthB H11 9 0.337 0.147 1.061 0.0000 0.0000 0.0000 2EthB H12 10 0.086 0.132 1.388 0.0000 0.0000 0.0000 2EthB H13 11 0.086 0.132 1.564 0.0000 0.0000 0.0000 2EthB C2 12 0.282 0.110 1.476 0.0000 0.0000 0.0000 2EthB H21 13 0.086 0.449 0.580 0.0000 0.0000 0.0000 2EthB H22 14 0.282 0.427 0.492 0.0000 0.0000 0.0000 3EthB C1 15 0.337 0.464 0.405 0.0000 0.0000 0.0000 3EthB H11 16 0.086 0.449 0.732 0.0000 0.0000 0.0000 To me what I have done is not right. 1- I am replicating CH3CH, while what I need is CH2CH2. Even when I do this I need to somehow add in CH3 to both ends! Please guide me on this issue 2- I am sure something is wrong. When I use -box 5 I get 8875 monomer units! Thank you, Moeed
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