[gmx-users] building up a long polymer chain

[Justin A. Lemkul]

Moeed wrote:
> Hello Justin,
> 
> I created structure file for a 4-carbon repeating unit as follows:
> HETATM    1  CAA DRG     1      14.260  -4.270   0.000  1.00 
> 20.00             C
> HETATM    2 1HAA DRG     1      14.175  -3.426   0.530  1.00 
> 20.00             H
> HETATM    3 2HAA DRG     1      15.050  -4.790   0.326  1.00 
> 20.00             H
> HETATM    4 3HAA DRG     1      14.385  -4.045  -0.966  1.00 
> 20.00             H
> HETATM    5  CAB DRG     1      12.990  -5.110   0.170  1.00 
> 20.00             C
> HETATM    6 1HAB DRG     1      12.205  -4.581  -0.153  1.00 
> 20.00             H
> HETATM    7 2HAB DRG     1      12.871  -5.326   1.139  1.00 
> 20.00             H
> HETATM    8  CAC DRG     1      13.070  -6.410  -0.620  1.00 
> 20.00             C
> HETATM    9 1HAC DRG     1      13.855  -6.939  -0.297  1.00 
> 20.00             H
> HETATM   10 2HAC DRG     1      13.189  -6.194  -1.589  1.00 
> 20.00             H
> HETATM   11  CAD DRG     1      11.800  -7.250  -0.450  1.00 
> 20.00             C
> HETATM   12 1HAD DRG     1      11.885  -8.094  -0.980  1.00 
> 20.00             H
> HETATM   13 2HAD DRG     1      11.675  -7.475   0.516  1.00 
> 20.00             H
> HETATM   14 3HAD DRG     1      11.010  -6.730  -0.776  1.00 
> 20.00             H
> 
> I renamed the atoms and removed one hydrogen atoms from both ends to get 
> repeating unit. CH2CH2,
> 
> 1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds 
> the third H automatically. I dont know anyother way but removing the 
> third H from structure file by hand..
> 
> Then I mesaured the C1 To C4 distance which is 0.388 A.
> 
> editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic
> 
>  12
>     1DRG     C1    1   0.208   0.006   0.242
>     1DRG    H11    2   0.158   0.010   0.328
>     1DRG    H12    3   0.149  -0.030   0.170
>     1DRG     C2    4   0.255   0.148   0.203
>     1DRG    H21    5   0.305   0.143   0.116
>     1DRG    H22    6   0.314   0.184   0.274
>     1DRG     C3    7   0.133   0.240   0.186
>     1DRG    H31    8   0.083   0.245   0.272
>     1DRG    H32    9   0.074   0.204   0.114
>     1DRG     C4   10   0.179   0.382   0.147
>     1DRG    H41   11   0.239   0.418   0.218
>     1DRG    H42   12   0.230   0.378   0.060
>    0.38800   0.38800   0.38800
> 
> then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1
> 
> 2- The problem here is that one CH2 unit with 2 H atoms is falling on 
> the next repeating unit in the next box. i.e 4 H atoms and C atoms are 
> overlapping... as shown below:
> 
>  H H H *H H* H H H
>  | |  |  | |  | | |
>  C-C-C-*CC*-C-C-C  
>  | |  |  | | |  |  |
>  H H H *H H* H H H
> 
> Do you think I should use -d option?
> 

As I've said twice now, use either -box or -d to set an appropriately-sized unit 
cell.  If you've measured a C...C distance of 0.388 nm, you've left no space for 
the bond that will occur to the next unit, so naturally you're seeing overlap. 
You've simply made your box too small.

-Justin

> Please guide me..
> Thanks
> 
> 

-- 
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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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