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

[Justin Lemkul]

On 3/3/15 2:22 AM, soumadwip ghosh wrote:
> 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.
>

VMD guesses what it thinks the bonds are.  What you see is not definitive; the 
topology is.

-Justin

>
>
>   [ 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
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================