Dear Justin,<br><br>Thanks so much for your help. The structure looks almost fine now. <br><br>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 <b>on</b> 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?<br>
<br>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?<br>
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<pre class="western">editconf -f 4C.gro -o 4Cd.gro -princ -d 0.0584 -bt cubic
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<pre class="western">4Cd.gro<br></pre>Great Red Owns Many ACres of Sand <br> 4<br> 1Eth C1 1 0.445 0.268 0.252<br> 1Eth C2 2 0.308 0.199 0.252<br> 1Eth C3 3 0.196 0.304 0.252<br>
1Eth C4 4 0.058 0.238 0.252<br>
0.50416 0.50416 0.50416<br>
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<pre class="western">editconf -f 4Cd.gro -o 4Cdindex.gro -n index.ndx -princ</pre>
Great Red Owns Many ACres of Sand<br> 4<br> 1Eth C1 1 0.446 0.286 0.252<br> 1Eth C2 2 0.321 0.198 0.252<br> 1Eth C3 3 0.195 0.286 0.252<br> 1Eth C4 4 0.068 0.201 0.252<br>
0.50416 0.50416 0.50416<br>
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<pre class="western">genconf -f 4Cdindex.gro -o 4Cdindex-rep.gro -nbox 5 1 1
</pre><pre class="western"> 4Cdindex-rep: with residues renamed <br></pre> 20<br> 1EthB C1 1 0.446 0.286 0.252 0.0000 0.0000 0.0000<br> 1EthB C2 2 0.321 0.198 0.252 0.0000 0.0000 0.0000<br>
1EthB C3 3 0.195 0.286 0.252 0.0000 0.0000 0.0000<br> 1EthB C4 4 0.068 0.201 0.252 0.0000 0.0000 0.0000<br> 2Eth C1 5 0.950 0.286 0.252 0.0000 0.0000 0.0000<br> 2Eth C2 6 0.825 0.198 0.252 0.0000 0.0000 0.0000<br>
2Eth C3 7 0.699 0.286 0.252 0.0000 0.0000 0.0000<br> 2Eth C4 8 0.572 0.201 0.252 0.0000 0.0000 0.0000<br> 3Eth C1 9 1.454 0.286 0.252 0.0000 0.0000 0.0000<br> 3Eth C2 10 1.329 0.198 0.252 0.0000 0.0000 0.0000<br>
3Eth C3 11 1.203 0.286 0.252 0.0000 0.0000 0.0000<br> 3Eth C4 12 1.076 0.201 0.252 0.0000 0.0000 0.0000<br> 4Eth C1 13 1.958 0.286 0.252 0.0000 0.0000 0.0000<br> 4Eth C2 14 1.833 0.198 0.252 0.0000 0.0000 0.0000<br>
4Eth C3 15 1.707 0.286 0.252 0.0000 0.0000 0.0000<br> 4Eth C4 16 1.580 0.201 0.252 0.0000 0.0000 0.0000<br> 5EthE C1 17 2.463 0.286 0.252 0.0000 0.0000 0.0000<br> 5EthE C2 18 2.338 0.198 0.252 0.0000 0.0000 0.0000<br>
5EthE C3 19 2.212 0.286 0.252 0.0000 0.0000 0.0000<br> 5EthE C4 20 2.085 0.201 0.252 0.0000 0.0000 0.0000<br> 2.52080 0.50416 0.50416<br><br><font size="4"><b>with hdb file</b></font><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>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>gro file generated by pdb2gmx: first few lines<br>62<br> 1EthB C1 1 0.446 0.286 0.252<br> 1EthB H11 2 0.419 0.382 0.252<br> 1EthB H12 3 0.500 0.267 0.334<br>
1EthB H13 4 0.500 0.267 0.170<br> 1EthB C2 5 0.321 0.198 0.252<br> 1EthB H21 6 0.265 0.185 0.170<br> 1EthB H22 7 0.265 0.185 0.334<br> 1EthB C3 8 0.195 0.286 0.252<br>
1EthB H31 9 0.138 0.292 0.334<br> 1EthB H32 10 0.138 0.292 0.170<br> 1EthB C4 11 0.068 0.201 0.252<br> 1EthB H41 12 0.011 0.191 0.170<br> 1EthB H42 13 0.011 0.191 0.334<br>
2Eth C1 14 0.950 0.286 0.252<br><input type="hidden"><input type="hidden"><div>
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