Thank you for your useful information!
Best,
Francisco
El [DATE], "[NAME]" <[ADDRESS]> escribió:
>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 - 08:30:03 PDT
