<br>I dont know if the hdb file is correct. Actually I want to learn how it works. <br><br>1- Manual says the third columns are name of new H atoms (here, H1, H2). why are they not the same as those in rtp file (H11, H12). There is no H1 and H2 in rtp file (<a href="http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html">http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html</a><br>
)<br><br>Also the control atoms: for example for the frist row in Eth: <br><pre>H1        C1        C2        -C2</pre>
This means H1 is connected to C1. In manual I read the other two depend on the code selected. Can you please explain what is the logic behind the other two atoms (C2 and -C2 in the forst row for example)<br><br><pre>Eth        2<br>
2        6        H1        C1        C2        -C2<br>2        6        H2        C2        C1        +C1<br>EthB        2<br>3        4        H1        C1        C2        +C1<br>2        6        H2        C2        C1        +C1<br>EthE        2<br>2        6        H1        C1        C2        -C2<br>3        4        H2        C2        C1        -C2        <br></pre>2- If I want to use these residues (Eth, EthB..) then I do not need to include H atoms in my pdb file? The reason I am asking this, is because if I make a long chain using any software, I see H atoms in pdb file. and the reason I am inclined to use these residues is that they are easier to work with...<br>
<pre>ATOM 1 C1 EthB 1 1.000 1.540 0.000<br>ATOM 2 C2 EthB 1 2.456 2.041 0.000<br>ATOM 3 C1 Eth 2 2.456 3.581 0.000<br>ATOM 4 C2 Eth 2 3.912 4.083 0.000<br>
ATOM 5 C1 EthE 3 3.912 5.623 0.000<br>ATOM 6 C2 EthE 3 5.368 6.124 0.000<br></pre><br>3- since I will have to work with very long polymer chains (1000 monomer units) what is the best approach or software to make such a chain. Some of the softwares do not do atmo numbering properly (or lack residues names) and I have to make a a lot of changes manually which is a nightmare for big chains.<br>
<br>Thanks,<br>Moeed<br><input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML"></div>