[AMBER] GAFF angle term constants with phosphor or sulphur

From: Igor Marques <igor.dragon88.gmail.com>
Date: Tue, 8 Oct 2013 14:30:49 +0100

Dear AMBER developers,

 Concerning the GAFF force-field, we noticed that angles containing
phosphor or sulphur atoms (x-px-x, x-x-px, x-sx-x, x-x-sx) present
different angle bending force constants when comparing the *gaff.dat* files
available in AMBERTOOLS13 and AMBERTOOLS1.2.

 To our understanding, this difference arises from Table 4 of the original
GAFF paper (J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A.
Case, *J. Comput. Chem.*, 2004, *25*, 1157-1174.), where the Z and C values
for phosphor and sulphur appear to be switched.

 This conclusion was achieved from testing 20 angles (given below) for
which each angle bending force constant was calculated applying the
equation presented in the Erratum (J. Wang, R. M. Wolf, J. W. Caldwell, P.
A. Kollman and D. A. Case, *J. Comput. Chem.*, 2005, *26*, 114-114.). The
estimated values matched the corresponding values in *gaff.dat* of
AMBERTOOLS1.2, but were different from the values of the *gaff.dat* of
AMBERTOOLS13. To obtain the angle bending force constants present in this
version of *gaff.dat*, the Z and C values of phosphor and sulphur had to be
exchanged.

 So, what is wrong? Is it the *gaff.dat* of AMBERTOOLS1.2 and, therefore,
Table 4 of the GAFF paper, OR is it the new *gaff.dat* of AMBERTOOLS13?



Best regards,

Igor





List of tested angles:

oh-p5-oh

oh-p5-o

c1-p3-hp

o -p5-o

c -p2-c2

p5-oh-ho

c3-os-py

h1-c3-p5

n -c3-p5

f -c3-p5

n -s4-o

i -s4-o

c3-sh-hs

oh-s6-oh

ce-sy-ce

ne-c1-s

h2-c3-s6

c1-n1-s4

c3-c -s4

nh-cd-ss

 Igor Marques, PhD Student
MSc in Pharmaceutical Biomedicine
BSc in Biomedical Sciences

Molecular Modeling Group University of
Aveirohttp://molecular-modeling.dq.ua.pt/

Mobile phone: +351 918 567 294
Landline: +351 234 247 254
Through PBX: +351 234 370 200 (ext. 22160)

Universidade de Aveiro
Campus Universitario de Santiago
Agra do Crasto Edificio 30
3810-193 Aveiro - Portugal
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Received on Tue Oct 08 2013 - 07:00:04 PDT
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