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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