[gmx-users] building up a long polymer chain

[Justin A. Lemkul]

Moeed wrote:
> 
> Hello Justin,
> 
> As you pointed out at the end of former message my real problem is 
> generation of a properly formatted structure file for PE. Within last 
> few weeks I tried to obtain the structure file using that known link... 
> but that was not helpful to me since those residues need atom 
> numbering..Hdb file was not helpful either because I think I need to 
> have a structure file with only coordinates of carbon atoms (hdb adds H 
> ). ...That coordinate file I dont know how to get.
> 

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

With both PRODRG and xLeap you should be able to easily build a short repeat 
unit.  You will have to rename the constituent atoms, but at least the 
coordinate files are syntactically correct.

> I tried x2top command to generate top file and I got LINCS error. I 
> followd the tips you had given before on how to diagnose a crashing 
> system and thats why I suspect top file is not produced properly when I 
> have no atom numbering in coordinate file. Now I am following your 

Well, I have never dealt with something like that, but if you're coordinate file 
is useless, then so too will the topology, likely.

> suggestion to use genconf command to build up my polymer. The distance 
> between C -C atoms in ethylene is 1.52 A. So I considred 0.76 A as 
> distance from each side, and 1.52+ 2*0.76=3.04 A as box size. In the 
> command line below I entered 0.304 to convert to nm. Please see below:
> 
> Initsial pdb file:
> 
> HETATM    1  C1  EthB    1      2.739   2.554  -0.012  0.00 
> -0.39           C
> HETATM    2  H11 EthB    1      2.736   3.644  -0.012  0.00  
> 0.13           H
> HETATM    3  H12 EthB    1      2.190   2.217  -0.893  0.00  
> 0.13           H
> HETATM    4  H13 EthB    1      2.190   2.217   0.868  0.00  
> 0.13           H
> HETATM    5  C2  EthB    1      4.155   1.993  -0.012  0.00 
> -0.26           C
> HETATM    6  H21 EthB    1      4.696   2.362  -0.887  0.00  
> 0.13           H
> HETATM    7  H22 EthB    1      4.696   2.362   0.862  0.00  
> 0.13           H
> END
> 
> editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 0.304 0.304 
> -angles 90 90 90 -d 0.076
> 

Going by the nomenclature of the system we've been discussing for the last 
eternity, EthB is a "beginning" residue, i.e. CH3-CH2-, when what you want to be 
using is Eth, which is a -CH2-CH2- unit.  Once you've built the coordinate file, 
change the names of the beginning and end residues and process the structure 
with pdb2gmx to build back the right hydrogens.

By specifying both -box and -d, you are adding extra space in the box.  The use 
of -angles is not necessary, and somehow you are not getting a cubic box:

>    0.40260   0.31710   0.32810   0.00000   0.00000   0.00000   0.00000   
> 0.00000   0.00000
> 

The proper command for what you want is:

editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 -bt cubic

> 
> genconf -f PEmonomer.gro -sort  -o PEsort -nbox 5
> 
> I use -sort to align the molecule with X coordinate and want to 
> replicate 5 boxes. Am I using correctly the -sort option? What I get is:
> 
> 8875
>     1EthB    C1    1   0.086   0.132   0.252  0.0000  0.0000  0.0000
>     1EthB   H11    2   0.282   0.110   0.164  0.0000  0.0000  0.0000
>     1EthB   H12    3   0.337   0.147   0.077  0.0000  0.0000  0.0000
>     1EthB   H13    4   0.086   0.132   0.404  0.0000  0.0000  0.0000
>     1EthB    C2    5   0.086   0.132   0.580  0.0000  0.0000  0.0000
>     1EthB   H21    6   0.282   0.110   0.492  0.0000  0.0000  0.0000
>     1EthB   H22    7   0.086   0.132   1.236  0.0000  0.0000  0.0000
>     2EthB    C1    8   0.282   0.110   1.148  0.0000  0.0000  0.0000
>     2EthB   H11    9   0.337   0.147   1.061  0.0000  0.0000  0.0000
>     2EthB   H12   10   0.086   0.132   1.388  0.0000  0.0000  0.0000
>     2EthB   H13   11   0.086   0.132   1.564  0.0000  0.0000  0.0000
>     2EthB    C2   12   0.282   0.110   1.476  0.0000  0.0000  0.0000
>     2EthB   H21   13   0.086   0.449   0.580  0.0000  0.0000  0.0000
>     2EthB   H22   14   0.282   0.427   0.492  0.0000  0.0000  0.0000
>     3EthB    C1   15   0.337   0.464   0.405  0.0000  0.0000  0.0000
>     3EthB   H11   16   0.086   0.449   0.732  0.0000  0.0000  0.0000
> 
> To me what I have done is not right.
> 
> 1- I am replicating CH3CH, while what I need is CH2CH2. Even when I do 
> this I need to somehow add in CH3 to both ends! Please guide me on this 
> issue

See above.

> 2- I am sure something is wrong. When I use -box 5 I get 8875 monomer 
> units!
> 

Yes, because when a GROMACS command expects a vector quantity, and receives only 
a scalar, it is applied uniformly in all directions.  This is documented in the 
manual.  I also see no purpose whatsoever to using -sort.  What you need is:

genconf -f PEmonomer.gro -o PEchain.gro -nbox 5 1 1

-Justin

> Thank you,
> Moeed
> 

-- 
========================================

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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