Dear all,
When I try the "natural language" system to define nmropt restraints for
a generalized distance coordinate (see section 23.1.1 in the manual), I
always get the fatal error:
Error: Not enough atoms or groupings specified in restraint.
I have noticed this behaviour in the past with amber11 and amber12 (and
simply reverted to "iat"), but now I have revisited it; I think this
feature can be quite useful, e.g. when working with slightly different
systems in which the atom numbering changes, but the residue numbering
doesn't (such as mutant proteins.)
Details:
sander: Version 14.0
RST file:
&rst
restraint="coordinate(distance(:350.C5,:350.O7),1.0,distance(:350.C9,:350.C1
),-1.0)",
r1=-502.0,r2=-2.0,r3=-2.0,r4=498.0,
rk2=100,rk3=100,
/
I have also tried:
restraint="coordinate(distance( (:350.C5) (:350.O7) ),1.0,distance( (:350.C9)
(:350.C1) ),-1.0)"
Both
restraint="(distance( (:350.C5) (:350.O7) )"
and
restraint="(distance( (:350.C9) (:350.C1) )"
do work.
I haven't tried angles or torsions, but the generalized distance coordinate
clearly doesn't work, at least not as described in the manual.
For now, I'll go back to iat, but it would be nice if this could be fixed.
--Marc
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Received on Tue Dec 02 2014 - 02:00:02 PST
