AMBER Archive (2006)

Subject: Re: AMBER: SHAKE - ntc = 3

From: Jennie Thomas (
Date: Mon Jan 09 2006 - 16:38:24 CST

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

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-
>>ON 16.000 1.000
>>NO 14.000 0.000
>>ON-ON 500. 2.197
>>ON-NO 500. 1.269
>>ON-NO-ON 100. 120.0
>>ON-ON-ON 0. 60.
>>NO-ON-ON 0. 30.
>>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.
>> 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
>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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