AMBER Archive (2006)

Subject: RE: AMBER: SHAKE - ntc = 3

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jan 09 2006 - 16:51:01 CST

Dear Jennie,

The bonds are not defined by the frcmod file, this simply defines the
parameters for a given bond type. The bonds themselves are defined in Leap
from the templates (.lib files) or from what you manually specify. In order
to have the bonds you need added you will either have to create you own unit
that has the bonds you want or manually bond them yourself by either drawing
them in in the xleap edit window or using the bond command.

Then when you save the prmtop file it will have the bonds in it.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Jennie Thomas
> Sent: Monday, January 09, 2006 14:38
> To: amber_at_scripps.edu
> Subject: Re: AMBER: SHAKE - ntc = 3
>
> Thank you for this helpful comment. You are correct, I do
> not actually
> have O-O bonds defined for each of the nitrate ions. Using
> rdparm, only
> the three bonds for water and the N-O bonds are listed.
>
> Looking back at my frcmod file, I can't understand why the
> O-O bonds are
> not being defined. Any advice on how to force leap to
> recognize these
> bonds?
>
> With thanks,
> Jennie Thomas
>
>
>
> David A. Case wrote:
>
> >On Fri, Jan 06, 2006, Jennie Thomas wrote:
> >
> >
> >>I am running a simulation of NO3- in water using the
> following frcmod file:
> >>
> >>This is the additional/replacement parameter set for
> nitrate ion NO3-
> >>MASS
> >>ON 16.000 1.000
> >>NO 14.000 0.000
> >>
> >>BOND
> >>ON-ON 500. 2.197
> >>ON-NO 500. 1.269
> >>
> >>ANGLE
> >>ON-NO-ON 100. 120.0
> >>ON-ON-ON 0. 60.
> >>NO-ON-ON 0. 30.
> >>
> >>DIHE
> >>ON-ON-ON-ON 2 0.0 0.0 2.
> >>ON-ON-ON-NO 2 0.0 0.0 2.
> >>ON-ON-NO-ON 2 0.0 0.0 2.
> >>ON-NO-ON-ON 2 0.0 0.0 2.
> >>
> >>
> >>NONB
> >> NO 1.88 0.1700
> >> ON 1.80 0.160
> >>
> >>In my input file, I have specified ntc=3, so all of the
> bond lengths
> >>should be fixed. However the O-O bond length (averaged
> over time) is
> >>about 0.1 Angstroms shorter than the length specified in the force
> >>field
> >>
> >>
> >
> >Do you actually have bonds defined between all pairs of oxygen atoms?
> >(Use rdparm to list all bonds in the molecule to make sure).
> >
> >You should almost always set ntf = ntc, but I don't think(?)
> this should be
> >the cause of your problem. Still, setting ntf=3 will remove
> all bonds
> >from the energy term, and should help in debugging.
> >
> >If you really have defined bonds between all pairs of atoms,
> this is a very
> >difficult challenge for SHAKE, but it should work. And, you
> don't need to
> >run 100 ps to see what is happening: try a simulation of 20
> steps or so,
> >saving the trajectory on every step, and look closely at the
> structure on
> >every step.
> >
> >...good luck...dac
> >
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> >
> >
> >
>
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