AMBER Archive (2006)

Subject: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files]

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Wed May 03 2006 - 16:49:19 CDT

Thanks in advance for your continued help with my simulation. I forgot
to add, I am also this warning when building my system in leap:

1-4: angle 914 915 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 914 916 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 914 916 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 914 915 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 913 915 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 913 916 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 913 914 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 913 916 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 913 914 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 913 915 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 919 920 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 919 920 duplicates bond ('triangular' bond) or angle
('square' bond)

This is not a problem since the force constant is zero for the angle.
But, I think I actually need to remove this angle in order to run the
simulation to avoid the following error upon trying to do an energy
minimization:

 EXTRA POINTS: nnb too small!
 nnb,ntot = 3456 7776

Thanks for any help you can give!

With thanks,
Jennie

-------- Original Message --------
Subject: Re: AMBER: Question bonds and angles in frcmod and lib files
Date: Wed, 03 May 2006 10:26:55 -0700
From: Jennie Thomas <jenniet_at_uci.edu>
To: amber_at_scripps.edu
References: <200605031628.k43GS8gK2089819_at_guanine.cgl.ucsf.edu>

Thanks for your comment, I do want to change all of the instances of the
atom types involved. I'm running a relatively simple system with only
one of this instance. However, simply setting the force constant to
zero doesn't seem to work due to this nnb,ntot problem.

I'm pretty sure these are related, because when I revert to using a .lib
file without the bonds (only angles defined) the minimization runs.

Cheers,
Jennie

Bill Ross wrote:

>>>I'm trying to more completely understand the information contained in
>>>frcmod and lib files. I would like to change from using an angle to
>>>constrain the geometry of my molecule to using an artificial bond with a
>>>given force constant. I understand how to add a bond to both the lib
>>>file and to the frcmod file. However, I don't understand how to delete
>>>an angle from these files.
>>>
>>>
>>Generally, you effectively delete the angle term by (re-)defining that angle
>>potential with a force constant of zero.
>>
>>
>
>Be sure when modifying params that you intend to modify all instances
>of the atom types involved.
>
>Bill
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