> >> But I found the carbon atoms are moving a lot
> >
> > What kind of movement? (I see you are using constant volume, so
> > coordinate scaling would not be involved as it would be for
> > constant pressure.)
> >
> The six membered-like rings doesn't exist even though the actual
> monomer is the two carbon molecule.
You won't see bonds that aren't there. But this has no bearing
on the type of movement. You are implying the sheet is becoming
distorted, but it sounds like the problem is that you expect
nonexistent bonds to be displayed in some viewing program?
Why have a 2-carbon basic residue rather than a ring?
> ##bondByDistance gr 1.5
This explains how you got the long bonds. An alternative is to
use the 'bond' command in leap to set each bond. However, it seems
bondByDistance should have worked, and this may be worth debugging
for whoever is maintaining leap.
> >> and I gave 10->5000 and NaN
> >> error was coming out again.
> >
> > For the restraint weight? 5000 is very high, you could try 50.
>
> I tried 50, but it also gave me NaN error.
>
> > Also, I will suggest gradual warming again.
Remember this suggestion if you are stuck at some point.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 20 2010 - 12:00:04 PDT
