[gmx-users] structure file long chains

Moeed lecielll at googlemail.com
Thu Jun 10 04:16:25 CEST 2010

I dont know if the hdb file is correct. Actually I want to learn how it

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 (

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

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

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