Hi,
Bonds can't just break in MM simulations; my guess is the bond was never
properly created. First thing I would do is check that the bond is really
there. You can do this in either cpptraj or parmed. In cpptraj:
> bondinfo <mask>
In parmed.py:
> printBonds <mask>
Both commands will list all bonds involving atoms in <mask>. If the bond
does actually show up we'll need some more information about the actual
procedure you followed (i.e the commands you used). It may be that even if
the bond is there, if for some reason it was assigned a very long
equilibrium value or a weak force constant (or both) it may appear to
'break'.
Hope this helps,
-Dan
On Tue, Feb 18, 2014 at 9:04 PM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi, I used the bond command to bond 2 fragments of a molecule together.
> These 2 fragments have different residue numbers and are separated by TER
> in the pdb file. When I ran the simulation, the bond broke. How can I
> resolve it.? Thanks.
>
> Sent from my iPhone
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Feb 18 2014 - 22:00:04 PST
