Hi everybody,
I found a discrepancy in the sasa calculation
between gromacs versions 4.0.2 and 4.5.1.
For a trajectory generated by gmx 4.0.2. with AMBER force fiels,
I calculated the sasa values by using the g_sas module taken
from gromacs 4.0.2 (a) and gromacs 4.5.1 (b).
I list the results for three representative residues:
(a) (b)
res 1 0.58 0.35
res 2 1.10 1.05
res 3 0.27 0.05
I got a rough agreement by changing the probe radius
from 0.14 to 0.10 in g_sas from gromacs 5.4.1 (b'):
(a) (b')
res 1 0.58 0.66
res 2 1.10 1.00
res 3 0.27 0.34
Could you explain me the reason for such discrepancy?
Cheers,
Rocco
--
Dr Rocco Caliandro
Istituto di Cristallografia
Consiglio Nazionale delle Ricerche
via Amendola 122/o, 70126 Bari - Italy
Tel ++39 080 5929150
Fax ++39 080 5929170
rocco.calian...@ic.cnr.it
www.ic.cnr.it
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