Hello,
There's something that I don't understand with using restraints in
sander. I want to do umbrella sampling for a reaction. For that, I
define 3 distances between couples of atoms: d2, d3 and d4. I want to
restraint a combination of d2/d3/d4 but also to output individual values.
To do so, I have created the following DISANG file:
"""
# d2
&rst restraint = "distance(:1.C,:3.O)", r0 = 3.2, k0 = 0., /
# d3
&rst restraint = "distance(:3.O,:3.H1)", r0 = 1.0, k0 = 0., /
# d4
&rst restraint = "distance(:3.H1,:2.OP2)", r0 = 1.8, k0 = 0., /
# d3-d4
&rst restraint =
"coordinate(distance(:3.O,:3.H1),1.0,distance(:3.H1,:2.OP2),-1.0)",
r0 = 3.2, k0 = 0., /
# d2-(d3-d4)
&rst restraint = "coordinate(distance(:1.C,:3.O), 1.0,
distance(:3.O,:3.H1), -1.0, distance(:3.H1,:2.OP2), 1.0)",
r0 = 3.2, k0 = 0., /
"""
If I run sander (AmberTools15), it crashes with:
"""
Here are comments from the DISANG input file:
# d2
Error: Invalid atom or grouping specified in restraint.
restraint = "distance( :1.C :3.O )"
"""
What is surprising is that if I comment all &rst except one, all
individual restraints are OK (i.e., sander run correctly). If I use
together only d2, d3 and d4 for restraints, no problem also. But any
combination of 'coordinate' with a distance or both 'coordinate'
restraints together give an error with sander.
Any idea?
Gerald.
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Sat Oct 31 2015 - 10:30:02 PDT
