[gmx-users] building up a long polymer chain

[Moeed]

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.

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 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

 7
    1EthB    C1    1   0.141   0.166   0.164
    1EthB   H11    2   0.141   0.275   0.164
    1EthB   H12    3   0.086   0.132   0.076
    1EthB   H13    4   0.086   0.132   0.252
    1EthB    C2    5   0.282   0.110   0.164
    1EthB   H21    6   0.337   0.147   0.077
    1EthB   H22    7   0.337   0.147   0.251
   0.40260   0.31710   0.32810   0.00000   0.00000   0.00000   0.00000
0.00000   0.00000


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


Thank you,
Moeed
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