Re: [AMBER] GAFF angle term constants with phosphor or sulphur

From: James Murdock <>
Date: Mon, 14 Oct 2013 15:13:16 +0200

Dear Igor

I checked some of the angles you presented and verified your claims:
 AngleKr (AT1.2)Kr (AT13)
c3-sh-hs 44.90028.120
c3-c -s459.60075.480
So, which version of gaff.dat is correct?
----- Original Message -----
From: Igor Marques
Sent: 10/08/13 02:30 PM
To: AMBER Mailing List
Subject: [AMBER] GAFF angle term constants with phosphor or sulphur

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 Aveiro 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 _______________________________________________ AMBER mailing list
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Received on Mon Oct 14 2013 - 06:30:03 PDT
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