[gmx-users] Bond connectivity not found during visualization in VMD

[soumadwip ghosh]

Hi all,
        I have made an initial structure for simulating a hybrid of swCNT
and ssDNA using Tubegen software for swCNT. The force field I use is CHARMM
27. I have simulated the same DNA in this force field multiple times but
for inserting CNT in the system I modified the aminoacids.rtp file
according to the bond and atom types mentioned in the PDB I created. I used
the aromatic atomtype CA and HP for CNT which is consistent with
literature J. Chem. Phys. 136, 175101 (2012).

But there is one problem. When I want to visualize the .gro file of the
hybrid I can see the bonds between atoms in the DNA while the atoms in the
CNT are appearing as only spheres without any bond connection. I am using
VMD for visualizing the structures. I feel that there is some error in the
[bonds] directive in the aminoacids.rtp file a part of which is shown below.



 [ 1MY0 ]
   [ atoms ]

 H1      HP                0.141             1
 C1      CA               -0.111             2
 C28     CA               -0.011             3
 C29     CA               -0.010             4
 C56     CA               -0.003             5
 C57     CA               -0.001             6
 C84     CA               -0.002             7
 C85     CA               -0.002             8
C112     CA               -0.001             9
C113     CA               -0.001             10
C140     CA               -0.002             11
C141     CA               -0.002             12
C168     CA               -0.001             13
C169     CA               -0.003             14
C196     CA               -0.010             15
C197     CA               -0.011             16
C224     CA               -0.111             17
 H28     HP                0.141             18
C223     CA               -0.111             19
 H27     HP                0.141             20
C222     CA               -0.011             21
C221     CA               -0.011             22
C220     CA               -0.111             23
 H26     HP                0.141             24
C219     CA               -0.111             25
 and so on....

  [ bonds ]

  1    2
  2    1    3  251
  3    2    4  250
  4    3    5  213
  5    4    6  187
  6    5    7  212
  7    6    8  186
  8    7    9  161
  9    8   10  135
 10    9   11  160
 11   10   12  134
 12   11   13  109
 13   12   14   83
 14   13   15  108
 15   14   16   82
 16   15   17   57
 17   16   18   19
 18   17
 19   17   20   21
 20   19
 21   19   22   82
 22   21   23   79
 23   22   24   25
 24   23
 25   23   26   27
 26   25
 27   25   28   78
 28   27   29   75
 29   28   30   31
 30   29
 31   29   32   33

and so on...

Am I i observing this in VMD because I put the numbers of atoms instead of
atom names ( like C2, H1, C219 etc) in the .rtp file?

Also, has the generation of all-atom PDB/ united atom PDB got anything to
with it? I made united atom PDB by the way.

I really dont know how to avoid this strange observation. Any kind of help
will be truly appreciated.

Thanks for your time in advance

Soumadwip Ghosh
Research Fellow,
IITB, Mumbai,
India