On Fri, Apr 01, 2016, Francisco Corzana López wrote:
> I am trying to run MD simulations using residual dipolar coupling
> (RDC) as restraints in explicit water (see bellow the input and the
> RDC files). I use as starting “inpcrd” file a structure previously
> equilibrated in water at 300K.
> I would like to know if this protocol is correct. When I run the
> MD simulations, sander reads the file with the restraints (file
> rdcOpennew.txt, see bellow) but it says: “** No restraint defined **”.
I *think* the no restraints refers to ordinary NMR restraints, not RDC's. It
looks like to you don't have any of these.
To see what the RDC's are doing, look for "Alignment tensor" in the output,
which should be printed out the regular energies for each step. See
$AMBERHOME/test/rdc/gcg.dip.o.save for an example output file.
> I have seen in the example provided by AMBER ($AMBERHOME/test/rdc) that
> an extra file (RST.csa) is added in the restraint section. The authors
> say that the “csa” restraints are dummies, intended to match the RDC
> values.
That is for pseudo-csa restraints. Look at the "Run.dip" test case for just
using RDC restraints.
> On the other hand, is it necessary to kill the translational and
> rotational motion of the center-of-mass to keep the molecule aligned?
No. If the molecule moves (rotates, or changes shape), the alignment tensor
follows such motion. (Overall translation has no effect on RDC's)
...hope this helps...dac
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Received on Fri Apr 01 2016 - 06:30:04 PDT
