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Torsions in GAFF force field

Asked by , Edited by Eric Jang

Hello, I have a question regarding the gaff.dat file used in OpenBabel for energy calculations and setting up force fields. 



In OpenBabel, torsion terms seem to be defined in the format:
X -c -c -X    4    1.200       180.000           2.000
X -c -c1-X    2    0.000       180.000           2.000     
X -c -cg-X    2    0.000       180.000           2.000      same as X-c-c1-X 
X -c -ch-X    2    0.000       180.000           2.000     
X -c -c2-X    4    8.700       180.000           2.000      intrpol.bsd.on C6H6

Where the is are I J K L atoms defined. Near the bottom of this list though, there is a line break and the format changes slightly to be more explicit in definition of I J K L and the second column disappears (what does this value represent?).

X -o -c -o          1.1          180.          2.           JCC,7,(1986),230
X -X -c -o          10.5         180.          2.           JCC,7,(1986),230
X -X -ca-ha         1.1          180.          2.           bsd.on C6H6 nmodes
X -X -n -hn         1.1          180.          2.           JCC,7,(1986),230
X -X -n2-hn         1.1          180.          2.           JCC,7,(1986),230
X -X -na-hn         1.1          180.          2.           JCC,7,(1986),230
X -c3-n -c3         1.1          180.          2.           JCC,7,(1986),230

Are these the improper torsional terms or just a ‘exceptions’ list to the more general torsion terms? Furthermore, I noticed that there are duplicate atom-groups with different params:
c3-c3-c3-c3   1    0.18          0.0            -3.         Junmei et al, 1999
c3-c3-c3-c3   1    0.25        180.0            -2.         Junmei et al, 1999
c3-c3-c3-c3   1    0.20        180.0             1.         Junmei et al, 1999
How do I know which one to use?
Thanks!


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1 answer

1

mjw from Cambridge, United Kingdom

Please see the link:
http://ambermd.org/formats.html#parm.dat
This explains the format used in the file.

With respect to the terms that you describe as “duplicate atom groups with different params”, a single given torsion parameter can be synthesised from multiple cosine terms ( see p259 of http://ambermd.org/doc8/amber8.pdf ) and the use of the negative PN value is an indication that more terms are to be read in:

NOTE: If PN .lt. 0.0 then the torsional potential
is assumed to have more than one term, and the
values of the rest of the terms are read from the
next cards until a positive PN is encountered. The
negative value of pn is used only for identifying
the existence of the next term and only the
absolute value of PN is kept.


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