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



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

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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