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rajni_swamy

Member

Registered: 2020-06-21

Posts: 3

Cluster Creation in vmd

Hi...
To calculate the hirshfeld surface we are required to input *.pdb file which contains a cluster. This cluster is generated in vmd. I followed your video tutorial, but Gaussview closes when I create a super cell. My molecule has 56 atoms (C, H, N and O). Somehow I managed to save as pdb. But the super cell was looking awkward. I changed the parameters to match my xrd values. I followed your video step by step. I copied your script and pasted it in tk console. but I didn't get any fragment number for my central atom like how you got fragment 182. after the final step I got only 2 molecules in my cluster

my main molecule was also not in the center of the cluster. Where did I go wrong? Please clarify.

Dr.Rajni

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,758

Website

Re: Cluster Creation in vmd

If gview doesn't work, you can use Avogadro or VESTA to create supercell, both of them are freely available and easy to use.
I cannot give you detailed advice without having your pdb file of supercell. If possible, please upload compressed .pdb file of large enough supercell.

rajni_swamy

Member

Registered: 2020-06-21

Posts: 3

Re: Cluster Creation in vmd

I tried VESTA. When I load my cif file, I get a unit cell with 8 molecules whereas my Z=4. I checked the unit cell parameters and changed it according to my data. Monoclinic etc. but immediately my molecule breaks. I tried even the mol file but nothing much happens. Is Gaussview closing because of the large number of atoms (56)?
This is what I got in my cluster.pdb when I used VMD.

These first line is not the correct lattice parameter or space group.

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 O X 0 8.582 2.627 3.430 0.00 0.00 O
ATOM 2 N X 0 6.992 4.170 6.762 0.00 0.00 N
ATOM 3 C X 0 11.442 3.480 7.514 0.00 0.00 C
ATOM 4 H X 0 10.794 2.879 7.804 0.00 0.00 H
ATOM 5 C X 0 12.485 3.823 8.377 0.00 0.00 C
ATOM 6 H X 0 12.528 3.445 9.226 0.00 0.00 H
ATOM 7 C X 0 13.427 4.699 7.982 0.00 0.00 C
ATOM 8 H X 0 14.120 4.919 8.563 0.00 0.00 H
ATOM 9 C X 0 13.382 5.286 6.707 0.00 0.00 C
ATOM 10 C X 0 14.335 6.235 6.296 0.00 0.00 C
ATOM 11 H X 0 15.017 6.481 6.878 0.00 0.00 H
ATOM 12 C X 0 14.276 6.790 5.076 0.00 0.00 C
ATOM 13 H X 0 14.919 7.413 4.823 0.00 0.00 H
ATOM 14 C X 0 13.262 6.444 4.185 0.00 0.00 C
ATOM 15 H X 0 13.234 6.832 3.341 0.00 0.00 H
ATOM 16 C X 0 12.313 5.541 4.547 0.00 0.00 C
ATOM 17 H X 0 11.636 5.323 3.948 0.00 0.00 H
ATOM 18 C X 0 12.338 4.930 5.814 0.00 0.00 C
ATOM 19 C X 0 11.347 4.005 6.255 0.00 0.00 C
ATOM 20 C X 0 10.282 3.594 5.347 0.00 0.00 C
ATOM 21 H X 0 10.537 3.444 4.465 0.00 0.00 H
ATOM 22 C X 0 8.990 3.404 5.620 0.00 0.00 C
ATOM 23 C X 0 8.352 3.694 6.941 0.00 0.00 C
ATOM 24 H X 0 8.344 2.889 7.481 0.00 0.00 H
ATOM 25 H X 0 8.871 4.366 7.410 0.00 0.00 H
ATOM 26 C X 0 6.188 3.114 6.164 0.00 0.00 C
ATOM 27 H X 0 5.254 3.378 6.154 0.00 0.00 H
ATOM 28 H X 0 6.268 2.303 6.690 0.00 0.00 H
ATOM 29 C X 0 6.658 2.861 4.768 0.00 0.00 C
ATOM 30 C X 0 8.117 2.940 4.514 0.00 0.00 C
ATOM 31 C X 0 5.857 2.632 3.729 0.00 0.00 C
ATOM 32 H X 0 6.270 2.600 2.896 0.00 0.00 H
ATOM 33 C X 0 4.412 2.424 3.731 0.00 0.00 C
ATOM 34 C X 0 3.838 1.557 4.615 0.00 0.00 C
ATOM 35 H X 0 4.362 1.177 5.283 0.00 0.00 H
ATOM 36 C X 0 2.483 1.225 4.539 0.00 0.00 C
ATOM 37 H X 0 2.116 0.639 5.161 0.00 0.00 H
ATOM 38 C X 0 1.706 1.749 3.572 0.00 0.00 C
ATOM 39 H X 0 0.815 1.490 3.509 0.00 0.00 H
ATOM 40 C X 0 2.224 2.683 2.656 0.00 0.00 C
ATOM 41 C X 0 1.419 3.288 1.674 0.00 0.00 C
ATOM 42 H X 0 0.521 3.055 1.608 0.00 0.00 H
ATOM 43 C X 0 1.933 4.204 0.827 0.00 0.00 C
ATOM 44 H X 0 1.384 4.597 0.188 0.00 0.00 H
ATOM 45 C X 0 3.274 4.566 0.898 0.00 0.00 C
ATOM 46 H X 0 3.618 5.194 0.305 0.00 0.00 H
ATOM 47 C X 0 4.088 3.998 1.840 0.00 0.00 C
ATOM 48 H X 0 4.981 4.254 1.889 0.00 0.00 H
ATOM 49 C X 0 3.596 3.035 2.735 0.00 0.00 C
ATOM 50 C X 0 6.432 4.636 8.029 0.00 0.00 C
ATOM 51 H X 0 6.727 4.049 8.743 0.00 0.00 H
ATOM 52 H X 0 5.464 4.592 7.986 0.00 0.00 H
ATOM 53 C X 0 6.852 6.044 8.339 0.00 0.00 C
ATOM 54 H X 0 6.560 6.627 7.635 0.00 0.00 H
ATOM 55 H X 0 7.809 6.084 8.412 0.00 0.00 H
ATOM 56 H X 0 6.456 6.320 9.169 0.00 0.00 H
ATOM 57 O X 0 19.359 2.627 1.513 0.00 0.00 O
ATOM 58 N X 0 17.769 4.170 4.845 0.00 0.00 N
ATOM 59 C X 0 22.219 3.480 5.598 0.00 0.00 C
ATOM 60 H X 0 21.571 2.879 5.887 0.00 0.00 H
ATOM 61 C X 0 23.261 3.823 6.461 0.00 0.00 C
ATOM 62 H X 0 23.305 3.445 7.310 0.00 0.00 H
ATOM 63 C X 0 24.204 4.699 6.066 0.00 0.00 C
ATOM 64 H X 0 24.897 4.919 6.646 0.00 0.00 H
ATOM 65 C X 0 24.158 5.286 4.791 0.00 0.00 C
ATOM 66 C X 0 25.112 6.235 4.379 0.00 0.00 C
ATOM 67 H X 0 25.793 6.481 4.962 0.00 0.00 H
ATOM 68 C X 0 25.053 6.790 3.160 0.00 0.00 C
ATOM 69 H X 0 25.695 7.413 2.906 0.00 0.00 H
ATOM 70 C X 0 24.039 6.444 5.269 0.00 0.00 C
ATOM 71 H X 0 24.011 6.832 1.424 0.00 0.00 H
ATOM 72 C X 0 23.090 5.541 2.631 0.00 0.00 C
ATOM 73 H X 0 22.413 5.323 2.031 0.00 0.00 H
ATOM 74 C X 0 23.115 4.930 3.898 0.00 0.00 C
ATOM 75 C X 0 22.124 4.005 4.338 0.00 0.00 C
ATOM 76 C X 0 21.059 3.594 3.431 0.00 0.00 C
ATOM 77 H X 0 21.313 3.444 2.549 0.00 0.00 H
ATOM 78 C X 0 19.766 3.404 3.704 0.00 0.00 C
ATOM 79 C X 0 19.129 3.694 5.025 0.00 0.00 C
ATOM 80 H X 0 19.121 2.889 5.565 0.00 0.00 H
ATOM 81 H X 0 19.648 4.366 5.494 0.00 0.00 H
ATOM 82 C X 0 16.965 3.114 4.248 0.00 0.00 C
ATOM 83 H X 0 16.031 3.378 4.237 0.00 0.00 H
ATOM 84 H X 0 17.045 2.303 4.774 0.00 0.00 H
ATOM 85 C X 0 17.435 2.861 2.851 0.00 0.00 C
ATOM 86 C X 0 18.894 2.940 2.598 0.00 0.00 C
ATOM 87 C X 0 16.634 2.632 1.812 0.00 0.00 C
ATOM 88 H X 0 17.047 2.600 0.980 0.00 0.00 H
ATOM 89 C X 0 15.189 2.424 1.815 0.00 0.00 C
ATOM 90 C X 0 14.615 1.557 2.698 0.00 0.00 C
ATOM 91 H X 0 15.139 1.177 3.367 0.00 0.00 H
ATOM 92 C X 0 13.260 1.225 2.623 0.00 0.00 C
ATOM 93 H X 0 12.893 0.639 3.244 0.00 0.00 H
ATOM 94 C X 0 12.482 1.749 1.656 0.00 0.00 C
ATOM 95 H X 0 11.591 1.490 1.592 0.00 0.00 H
ATOM 96 C X 0 13.001 2.683 0.740 0.00 0.00 C
ATOM 97 C X 0 12.195 3.288 -0.242 0.00 0.00 C
ATOM 98 H X 0 11.298 3.055 -0.308 0.00 0.00 H
ATOM 99 C X 0 12.710 4.204 -1.090 0.00 0.00 C
ATOM 100 H X 0 12.161 4.597 -1.729 0.00 0.00 H
ATOM 101 C X 0 14.051 4.566 -1.018 0.00 0.00 C
ATOM 102 H X 0 14.395 5.194 -1.611 0.00 0.00 H
ATOM 103 C X 0 14.865 3.998 -0.076 0.00 0.00 C
ATOM 104 H X 0 15.757 4.254 -0.028 0.00 0.00 H
ATOM 105 C X 0 14.373 3.035 0.819 0.00 0.00 C
ATOM 106 C X 0 17.209 4.636 6.112 0.00 0.00 C
ATOM 107 H X 0 17.504 4.049 6.827 0.00 0.00 H
ATOM 108 H X 0 16.241 4.592 6.070 0.00 0.00 H
ATOM 109 C X 0 17.629 6.044 6.423 0.00 0.00 C
ATOM 110 H X 0 17.337 6.627 5.719 0.00 0.00 H
ATOM 111 H X 0 18.586 6.084 6.496 0.00 0.00 H
ATOM 112 H X 0 17.233 6.320 7.253 0.00 0.00 H
END

Last edited by rajni_swamy (2020-06-22 07:19:30)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,758

Website

Re: Cluster Creation in vmd

It is best to upload your .cif file, or send it privately to me via E-mail, I will check

rajni_swamy

Member

Registered: 2020-06-21

Posts: 3

Re: Cluster Creation in vmd

I have sent you private mail and attached cif file. This is Dr.Rajni Swamy.