Dear Justin, Thanks so much for your help. The structure looks almost fine now.
1-I am getting bond distance of 1.52 or 1.53 and angles of 112.2 / 112.0 with -d 0.0584/ 0.0581. Actually when I open up the same structure file in VMD at different times I see even a little difference in bond distance between atoms *on* the 4C unit chain (1.54 , 1.53 A). Thats why I though maybe 1 or 2 degrees difference from equilibrium value of 110 for connecting atoms does not influence results..But still I wanted to make sure if I need to do energy minimization to get exact value of 110 for angles between repeating units and if this is going to affect simulation results? 2- I am trying to obtain top and gro file including H atoms with hdb abd rtp files. I am not getting any error messages and it seems everything is going well but the gro file after adding H s has a very weird structure. I doubt I have wriiten hdb file correctly. Could you please take a look at it? editconf -f 4C.gro -o 4Cd.gro -princ -d 0.0584 -bt cubic 4Cd.gro Great Red Owns Many ACres of Sand 4 1Eth C1 1 0.445 0.268 0.252 1Eth C2 2 0.308 0.199 0.252 1Eth C3 3 0.196 0.304 0.252 1Eth C4 4 0.058 0.238 0.252 0.50416 0.50416 0.50416 editconf -f 4Cd.gro -o 4Cdindex.gro -n index.ndx -princ Great Red Owns Many ACres of Sand 4 1Eth C1 1 0.446 0.286 0.252 1Eth C2 2 0.321 0.198 0.252 1Eth C3 3 0.195 0.286 0.252 1Eth C4 4 0.068 0.201 0.252 0.50416 0.50416 0.50416 genconf -f 4Cdindex.gro -o 4Cdindex-rep.gro -nbox 5 1 1 4Cdindex-rep: with residues renamed 20 1EthB C1 1 0.446 0.286 0.252 0.0000 0.0000 0.0000 1EthB C2 2 0.321 0.198 0.252 0.0000 0.0000 0.0000 1EthB C3 3 0.195 0.286 0.252 0.0000 0.0000 0.0000 1EthB C4 4 0.068 0.201 0.252 0.0000 0.0000 0.0000 2Eth C1 5 0.950 0.286 0.252 0.0000 0.0000 0.0000 2Eth C2 6 0.825 0.198 0.252 0.0000 0.0000 0.0000 2Eth C3 7 0.699 0.286 0.252 0.0000 0.0000 0.0000 2Eth C4 8 0.572 0.201 0.252 0.0000 0.0000 0.0000 3Eth C1 9 1.454 0.286 0.252 0.0000 0.0000 0.0000 3Eth C2 10 1.329 0.198 0.252 0.0000 0.0000 0.0000 3Eth C3 11 1.203 0.286 0.252 0.0000 0.0000 0.0000 3Eth C4 12 1.076 0.201 0.252 0.0000 0.0000 0.0000 4Eth C1 13 1.958 0.286 0.252 0.0000 0.0000 0.0000 4Eth C2 14 1.833 0.198 0.252 0.0000 0.0000 0.0000 4Eth C3 15 1.707 0.286 0.252 0.0000 0.0000 0.0000 4Eth C4 16 1.580 0.201 0.252 0.0000 0.0000 0.0000 5EthE C1 17 2.463 0.286 0.252 0.0000 0.0000 0.0000 5EthE C2 18 2.338 0.198 0.252 0.0000 0.0000 0.0000 5EthE C3 19 2.212 0.286 0.252 0.0000 0.0000 0.0000 5EthE C4 20 2.085 0.201 0.252 0.0000 0.0000 0.0000 2.52080 0.50416 0.50416 *with hdb file* Eth 4 2 6 H1 C1 C2 -C4 2 6 H2 C2 C1 +C1 2 6 H3 C3 C2 +C1 2 6 H4 C4 C3 +C1 EthB 4 3 4 H1 C1 C2 +C1 2 6 H2 C2 C1 +C1 2 6 H3 C3 C2 +C1 2 6 H4 C4 C3 +C1 EthE 4 2 6 H1 C1 C2 -C4 2 6 H2 C2 C1 -C4 2 6 H3 C3 C2 -C4 3 4 H4 C4 C3 -C4 with rtp file: ; Polyethylene - this is an internal residue [ 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 C3 opls_136 -0.120 3 H31 opls_140 0.060 3 H32 opls_140 0.060 3 C4 opls_136 -0.120 4 H41 opls_140 0.060 4 H42 opls_140 0.060 4 [ bonds ] C1 -C4 C1 H11 C1 H12 C1 C2 C2 H21 C2 H22 C2 C3 C3 H31 C3 H32 C3 C4 C4 H41 C4 H42 C4 +C1 ; Terminal PE residue ("beginning" of chain) ; designation arbitrary, C1 is -CH3 [ EthB ] [ atoms ] C1 opls_135 -0.180 1 H11 opls_140 0.060 1 H12 opls_140 0.060 1 H13 opls_140 0.060 1 C2 opls_136 -0.120 2 H21 opls_140 0.060 2 H22 opls_140 0.060 2 C3 opls_136 -0.120 3 H31 opls_140 0.060 3 H32 opls_140 0.060 3 C4 opls_136 -0.120 4 H41 opls_140 0.060 4 H42 opls_140 0.060 4 [ bonds ] C1 H11 C1 H12 C1 H13 C1 C2 C2 H21 C2 H22 C2 C3 C3 H31 C3 H32 C3 C4 C4 H41 C4 H42 C4 +C1 ; Terminal PE residue ("end" of chain) ; designation arbitrary, C2 is -CH3 [ EthE ] [ 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 C3 opls_136 -0.120 3 H31 opls_140 0.060 3 H32 opls_140 0.060 3 C4 opls_136 -0.120 4 H41 opls_140 0.060 4 H42 opls_140 0.060 4 H43 opls_140 0.060 4 [ bonds ] C1 -C4 C1 H11 C1 H12 C1 C2 C2 H21 C2 H22 C2 C3 C3 H31 C3 H32 C3 C4 C4 H41 C4 H42 C4 H43 gro file generated by pdb2gmx: first few lines 62 1EthB C1 1 0.446 0.286 0.252 1EthB H11 2 0.419 0.382 0.252 1EthB H12 3 0.500 0.267 0.334 1EthB H13 4 0.500 0.267 0.170 1EthB C2 5 0.321 0.198 0.252 1EthB H21 6 0.265 0.185 0.170 1EthB H22 7 0.265 0.185 0.334 1EthB C3 8 0.195 0.286 0.252 1EthB H31 9 0.138 0.292 0.334 1EthB H32 10 0.138 0.292 0.170 1EthB C4 11 0.068 0.201 0.252 1EthB H41 12 0.011 0.191 0.170 1EthB H42 13 0.011 0.191 0.334 2Eth C1 14 0.950 0.286 0.252
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