Hello Justin, I think I did not convey my problem properly in the former message. Please help me with the following 2 questions:
I am actually having problem with geometry of C atoms at the end of one monomer unit and C at the beginning of the next unit. I am trying to replicate 4-carbon monomer. The C s on the backbone have sp3 geometry but when I put the second unit after the first, 4th and 5th dont have sp3 geometry. Before I said I got the 1.53A bond distance between C 4 and 5 by changing the box size by try and error and you mentioned, there should be no try and error. I guess you thought I am talking bout C s on the chain. Since structure is tetrahedral it is not like that I specify the the gap between the molecule and wall by taking into account just the half of the bond length. Apart from the distance, I have no control on the angle between C 4 and 5 either. Replicating using genconf does not give right geometry for connecting C atoms. Q1- So actually I was asking you if there is any way to set a proper bond length and angle between 4-C repeating units since I am doing this by changing the box size. When connecting atoms ( C 4 and 5 in case of first and second repeating units) get close I am not getting the 110 angle ( this is actually the angle between carbons on the chain). What I do is: editconf -f 4C.pdb -o 4C430.gro -box 0.430 -bt cubic genconf -f 4C430.gro -o 4C430rep.gro -nbox 5 1 1 4C430.gro: 4 1Eth C1 1 0.392 0.194 0.291 1Eth C2 2 0.276 0.174 0.193 1Eth C3 3 0.154 0.255 0.237 1Eth C4 4 0.037 0.237 0.140 0.43000 0.43000 0.43000 5 boxes replicated: and renamed the residues 1 and last. 4C430rep.gro 20 1EthB C1 1 0.392 0.194 0.291 0.0000 0.0000 0.0000 1EthB C2 2 0.276 0.174 0.193 0.0000 0.0000 0.0000 1EthB C3 3 0.154 0.255 0.237 0.0000 0.0000 0.0000 1EthB C4 4 0.037 0.237 0.140 0.0000 0.0000 0.0000 2Eth C1 5 0.822 0.194 0.291 0.0000 0.0000 0.0000 2Eth C2 6 0.706 0.174 0.193 0.0000 0.0000 0.0000 2Eth C3 7 0.584 0.255 0.237 0.0000 0.0000 0.0000 2Eth C4 8 0.467 0.237 0.140 0.0000 0.0000 0.0000 3Eth C1 9 1.252 0.194 0.291 0.0000 0.0000 0.0000 3Eth C2 10 1.136 0.174 0.193 0.0000 0.0000 0.0000 3Eth C3 11 1.014 0.255 0.237 0.0000 0.0000 0.0000 3Eth C4 12 0.897 0.237 0.140 0.0000 0.0000 0.0000 4Eth C1 13 1.682 0.194 0.291 0.0000 0.0000 0.0000 4Eth C2 14 1.566 0.174 0.193 0.0000 0.0000 0.0000 4Eth C3 15 1.444 0.255 0.237 0.0000 0.0000 0.0000 4Eth C4 16 1.327 0.237 0.140 0.0000 0.0000 0.0000 5EthE C1 17 2.112 0.194 0.291 0.0000 0.0000 0.0000 5EthE C2 18 1.996 0.174 0.193 0.0000 0.0000 0.0000 5EthE C3 19 1.874 0.255 0.237 0.0000 0.0000 0.0000 5EthE C4 20 1.757 0.237 0.140 0.0000 0.0000 0.0000 2.15000 0.43000 0.43000 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 and 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 then: pdb2gmx -f 4C430rep.gro -o 4C430repgmx.gro -p 4C430repgmx.top -ff oplsaa >& output.pdb2gmx Q2- What I am getting is a top file but gro file processed with hdb and rtp gives a very weird structure which has nothing to do with PE chain. Thanks for your attention. Moeed
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