> >> >> 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?
> >
> I just expected all the two-carbon residues are on the plain not distorted.
It's still hard to get a sense of how distorted it is. If you
watch the movie of the mdcrd, it should show that the atoms
remain centered on their original positions although moving
around, where increasing the force constant would lead to faster,
smaller movement. Also, rapid warming such as you are doing might
lead to more erratic fluctuations at first, but these should subside
over time.
One way to show the extent of fluctuations numerically would be to
use ptraj to get the RMS over time - it should remain constant.
But having just pairs of atoms bonded will make for some unnatural
asymmetry to the fluctuations.
> > Why have a 2-carbon basic residue rather than a ring?
> >
> Becuase I failed to generate prepi by using antechamber with more than
> two-carbon monomer.
Eventually I think you need to have all bonds, or none (which would be
a cruder approximation of the sheet). If you can get more bonds into your
residue unit, it means less to make by other means.
> >> ##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.
> >
> If I simply use 'bond' command, I need to specify all atom numbers.
> But I have more than 2000 carbon atoms finally and there is no way to
> pair carbon indices.
Possibly you could get the bonds by creating your model in a
program that will generate them somehow (likely the equivalent of
bondbydistance), then save as pdb with CONECT records to load into
leap.
More complicated would be to write a program that would output a
leap script with all the needed bond cmds. Maybe easier than that
would be to debug bondByDistance.
Finally, you could draw the bonds manually in xleap, or use
bondbydistance and then delete the extra bonds.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 20 2010 - 14:30:04 PDT
