> On Feb 23, 2014, at 10:04 AM, Zahra Khatti <khatti_za.yahoo.com> wrote:
>
> I used antechamber and parmchk to add missing parameters for Pt,
> steepest desent and conjugate gradiant algorithm for minimization.
>
>
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 2000,
> ntb = 1,
> ntr = 0,
> cut = 12.0
> /
>
Bonds cannot break in the Amber force field. It is simply not possible. If it appears that bonds are breaking then one of three things are happening.
1) the bond is not present in the topology file in the first place.
2) the bond force constant is far too weak, allowing it to stretch way too far (and making it look like bonds are "breaking"). Alternatively, the equilibrium length is too long.
3) the starting geometry is very bad, resulting in very high forces that distort the structure.
You can use parmed with the printBonds command to inspect what bonds exist and what their parameters are. You can find information about how to use this in the AmberTools manual or with the help command in parmed.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 23 2014 - 08:00:03 PST
