I dont know if the hdb file is correct. Actually I want to learn how it works.
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 ( http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html ) Also the control atoms: for example for the frist row in Eth: H1 C1 C2 -C2 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) Eth 2 2 6 H1 C1 C2 -C2 2 6 H2 C2 C1 +C1 EthB 2 3 4 H1 C1 C2 +C1 2 6 H2 C2 C1 +C1 EthE 2 2 6 H1 C1 C2 -C2 3 4 H2 C2 C1 -C2 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... ATOM 1 C1 EthB 1 1.000 1.540 0.000 ATOM 2 C2 EthB 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 EthE 3 3.912 5.623 0.000 ATOM 6 C2 EthE 3 5.368 6.124 0.000 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. Thanks, Moeed
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