Hello Justin,<br><br>I think I did not convey my problem properly in the former message. Please help me with the following 2 questions:<br><br>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.<br>
<br>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).<br>
<br><br>What I do is:<br>
<br>editconf -f 4C.pdb -o 4C430.gro -box 0.430 -bt cubic<br>
genconf -f 4C430.gro -o 4C430rep.gro -nbox 5 1 1<br><br> 4C430.gro:<br> 4<br> 1Eth C1 1 0.392 0.194 0.291<br> 1Eth C2 2 0.276 0.174 0.193<br> 1Eth C3 3 0.154 0.255 0.237<br>
1Eth C4 4 0.037 0.237 0.140<br> 0.43000 0.43000 0.43000<br><br> 5 boxes replicated: and renamed the residues 1 and last.<br>4C430rep.gro<br>20<br> 1EthB C1 1 0.392 0.194 0.291 0.0000 0.0000 0.0000<br>
1EthB C2 2 0.276 0.174 0.193 0.0000 0.0000 0.0000<br> 1EthB C3 3 0.154 0.255 0.237 0.0000 0.0000 0.0000<br> 1EthB C4 4 0.037 0.237 0.140 0.0000 0.0000 0.0000<br> 2Eth C1 5 0.822 0.194 0.291 0.0000 0.0000 0.0000<br>
2Eth C2 6 0.706 0.174 0.193 0.0000 0.0000 0.0000<br> 2Eth C3 7 0.584 0.255 0.237 0.0000 0.0000 0.0000<br> 2Eth C4 8 0.467 0.237 0.140 0.0000 0.0000 0.0000<br> 3Eth C1 9 1.252 0.194 0.291 0.0000 0.0000 0.0000<br>
3Eth C2 10 1.136 0.174 0.193 0.0000 0.0000 0.0000<br> 3Eth C3 11 1.014 0.255 0.237 0.0000 0.0000 0.0000<br> 3Eth C4 12 0.897 0.237 0.140 0.0000 0.0000 0.0000<br> 4Eth C1 13 1.682 0.194 0.291 0.0000 0.0000 0.0000<br>
4Eth C2 14 1.566 0.174 0.193 0.0000 0.0000 0.0000<br> 4Eth C3 15 1.444 0.255 0.237 0.0000 0.0000 0.0000<br> 4Eth C4 16 1.327 0.237 0.140 0.0000 0.0000 0.0000<br> 5EthE C1 17 2.112 0.194 0.291 0.0000 0.0000 0.0000<br>
5EthE C2 18 1.996 0.174 0.193 0.0000 0.0000 0.0000<br> 5EthE C3 19 1.874 0.255 0.237 0.0000 0.0000 0.0000<br> 5EthE C4 20 1.757 0.237 0.140 0.0000 0.0000 0.0000<br> 2.15000 0.43000 0.43000<br>
<br>with rtp file:<br><br>; Polyethylene - this is an internal residue<br>[ Eth ]<br> [ atoms ]<br> C1 opls_136 -0.120 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> C2 opls_136 -0.120 2<br>
H21 opls_140 0.060 2<br> H22 opls_140 0.060 2<br> C3 opls_136 -0.120 3<br> H31 opls_140 0.060 3<br> H32 opls_140 0.060 3<br> C4 opls_136 -0.120 4<br> H41 opls_140 0.060 4<br>
H42 opls_140 0.060 4<br><br> [ bonds ]<br> C1 -C4<br> C1 H11<br> C1 H12<br> C1 C2<br> C2 H21<br> C2 H22<br> C2 C3<br> C3 H31<br> C3 H32<br> C3 C4<br> C4 H41<br>
C4 H42<br> C4 +C1<br>; Terminal PE residue ("beginning" of chain)<br>; designation arbitrary, C1 is -CH3<br>[ EthB ]<br> [ atoms ]<br> C1 opls_135 -0.180 1<br> H11 opls_140 0.060 1<br>
H12 opls_140 0.060 1<br> H13 opls_140 0.060 1<br> C2 opls_136 -0.120 2<br> H21 opls_140 0.060 2<br> H22 opls_140 0.060 2<br> C3 opls_136 -0.120 3<br> H31 opls_140 0.060 3<br>
H32 opls_140 0.060 3<br> C4 opls_136 -0.120 4<br> H41 opls_140 0.060 4<br> H42 opls_140 0.060 4<br><br> [ bonds ]<br> C1 H11<br> C1 H12<br> C1 H13<br> C1 C2<br>
C2 H21<br> C2 H22<br> C2 C3<br> C3 H31<br> C3 H32<br> C3 C4<br> C4 H41<br> C4 H42<br> C4 +C1<br><br>; Terminal PE residue ("end" of chain)<br>; designation arbitrary, C2 is -CH3<br>
[ EthE ]<br> [ atoms ]<br> C1 opls_136 -0.120 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> C2 opls_136 -0.120 2<br> H21 opls_140 0.060 2<br> H22 opls_140 0.060 2<br>
C3 opls_136 -0.120 3<br> H31 opls_140 0.060 3<br> H32 opls_140 0.060 3<br> C4 opls_136 -0.120 4<br> H41 opls_140 0.060 4<br> H42 opls_140 0.060 4<br> H43 opls_140 0.060 4<br>
<br> [ bonds ]<br> C1 -C4<br> C1 H11<br> C1 H12<br> C1 C2<br> C2 H21<br> C2 H22<br> C2 C3<br> C3 H31<br> C3 H32<br> C3 C4<br> C4 H41<br> C4 H42<br> C4 H43<br>
<br>and with hdb file:<br>Eth 4<br>2 6 H1 C1 C2 -C4<br>2 6 H2 C2 C1 +C1<br>2 6 H3 C3 C2 +C1<br>2 6 H4 C4 C3 +C1<br>
EthB 4<br>3 4 H1 C1 C2 +C1<br>2 6 H2 C2 C1 +C1<br>2 6 H3 C3 C2 +C1<br>2 6 H4 C4 C3 +C1<br>EthE 4<br>2 6 H1 C1 C2 -C4<br>
2 6 H2 C2 C1 -C4<br>2 6 H3 C3 C2 -C4<br>3 4 H4 C4 C3 -C4<br><br>then: <br>
pdb2gmx -f 4C430rep.gro -o 4C430repgmx.gro -p 4C430repgmx.top -ff oplsaa >& output.pdb2gmx<br>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.<br>
<br>Thanks for your attention.<br>Moeed<br><br><br><br><br><br><br><br><br><input type="hidden"><input type="hidden"><div>
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