[gmx-users] structure file long chains

[Justin A. Lemkul]

Moeed wrote:
> 
> I dont know if the hdb file is correct. Actually I want to learn how it 
> works.
> 

The .hdb file works.  I've used it :)  Did you try it yourself with the examples 
posted?

> 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
> )
> 

H1 and H2 are the base names.  Since 2 of each are added, 1 and 2 get appended 
to these names -> H11, H12, H21, and H22.

> 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)
> 

Look at the amino acids for examples.  The +/- convention means "previous" and 
"next" residue, respectively (like a peptide backbone).

> 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 

Correct.  That's the purpose of the .hdb file.

> 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...
> 

It's up to you what you use.  If you can produce an all-atom structure, then you 
don't need to rely on the .hdb file to add hydrogens for you.  If you generate 
only C atoms, then the .hdb file will add the necessary hydrogens.

> 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.
> 

I don't have any suggestions beyond the link I posted already.  Maybe someone 
who routinely deals with polymers can comment on this one.

-Justin

> Thanks,
> Moeed
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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