AMBER Archive (2008)

Subject: RE: AMBER: to understand how frcmod.ff99SB works

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 28 2008 - 11:59:09 CDT

Hi Alan,

 

Amber allows multiple dihedrals but only if the periodicity is different for each dihedral. So in the case below the -4 and -3 periodicity entries are added as additional dihedrals while the -2 and 1 entries in frcmod.ff99SB should overwrite the existing two entries from parm99.dat.

 

Loading any additional parameters with the same atom types and matching periodicities will overwrite existing entries already loaded that match that atom type set and periodicity. Hence why FF99SB has

 

C -N -CT-C 1 0.00 0.0 1.

 

This is equivalent of deleting the original 0.8 barrier height dihedral from parm99.dat.

 

I hope this helps,

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Alan
Sent: Thursday, August 28, 2008 3:29 AM
To: amber_at_scripps.edu
Subject: AMBER: to understand how frcmod.ff99SB works

 

Dears,

 

So, I would like to understand what exactly is happening to parameters when you load from frcmod.ff99SB.

 

So in tleap, loading leaprc.ff99SB, it will first load parm99.dat and then frcmod.ff99SB. Taking a set o parameter to illustrate, we have in parm99.dat, DIHE:

 

C -N -CT-C 1 0.850 180.000 -2.

C -N -CT-C 1 0.800 0.000 1.

 

Looking at frcmod.ff99SB, we have:

 

C -N -CT-C 1 0.00 0.0 -4. four amplitudes and

C -N -CT-C 1 0.42 0.0 -3. phases for phi

C -N -CT-C 1 0.27 0.0 -2.

C -N -CT-C 1 0.00 0.0 1.

 

So what exactly is happening here? Are those 4 new entries added to the 2 first original or the simply replacing them?

 

Many thanks in advance.

 

Cheers,

Alan 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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