>
> Are the missing bonds in VMD between two different molecules (i.e. with
> different chain ID's, or with a TER card between them)?
>
BKB (on the enzyme backbone) is bonded to the active center MOL by commands
on leap. Below an excerpt from the leap-saved pdb showing one of the six
BKBs and the active center MOL. All BKBs come before MOL.
TER lines separate MOL, to avoid it connecting to pdb neighbors.
What follows MOL (i.e., from residue 500 on) are other protein chains not
involved with the enzyme active center.
.......................................
.........................................
TOM 1624 C GLY 102 10.158 -38.845 16.994 1.00 0.00
ATOM 1625 O GLY 102 11.039 -38.847 17.852 1.00 0.00
ATOM 1626 N BKB 103 10.074 -39.789 16.060 1.00 0.00
ATOM 1627 H BKB 103 9.276 -39.814 15.442 1.00 0.00
ATOM 1628 CA BKB 103 11.118 -40.811 15.895 1.00 0.00
ATOM 1629 HA BKB 103 11.186 -41.411 16.802 1.00 0.00
ATOM 1630 C BKB 103 12.444 -40.120 15.636 1.00 0.00
ATOM 1631 O BKB 103 13.444 -40.475 16.210 1.00 0.00
ATOM 1632 N TYR 104 12.436 -39.102 14.774 1.00 0.00
ATOM 1633 H TYR 104 11.571 -38.825 14.333 1.00 0.00
.....................................
...........................................
ATOM 7890 C SER 498 -46.922 -36.935 4.818 1.00 0.00
ATOM 7891 O SER 498 -47.076 -35.731 5.043 1.00 0.00
ATOM 7892 OXT SER 498 -47.165 -37.108 3.611 1.00 0.00
TER
ATOM 7893 C2 MOL 499 8.945 -43.533 14.747 1.00 0.00
ATOM 7894 H5 MOL 499 8.828 -42.641 14.113 1.00 0.00
ATOM 7895 H6 MOL 499 9.994 -43.572 15.057 1.00 0.00
.........................................
......................................
ATOM 7961 O MOL 499 9.274 -46.967 18.219 1.00 0.00
ATOM 7962 OXT MOL 499 9.878 -46.375 20.314 1.00 0.00
TER
ATOM 7963 N SER 500 -13.260 -17.899 7.054 1.00 0.00
ATOM 7964 H1 SER 500 -12.889 -18.710 7.528 1.00 0.00
............................................
............................................
Thanks for your interest
francesco
On Sat, Jan 17, 2015 at 3:55 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Fri, Jan 16, 2015, Francesco Pietra wrote:
>
> > if ParmEd reports that a bond exists, then the prmtop defines
> > that bond... VMD *should* report all bonds when loading a prmtop
>
> Are the missing bonds in VMD between two different molecules (i.e. with
> different chain ID's, or with a TER card between them)? Or, is there
> anything
> that is different about the bonds that VMD shows and the ones that it
> misses?
> Can you make a small example that illustrates the problem?
>
> ...dac
>
>
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Received on Sat Jan 17 2015 - 08:00:03 PST
