Re: [AMBER] Changes in DNA sugar chilarity at NMR volume restrained simulation

From: David A Case <>
Date: Thu, 12 Nov 2020 08:27:06 -0500

On Thu, Nov 12, 2020, lomzov wrote:
>I am refining the duplex DNA structure using NOESY volume restraints and
>restrained molecular dynamics simulations. In some cases, at a high
>restraining potential (35 kcal), changes in sugar chirality (C1', C2',
>C3' or C4' atoms) were observed during the simulation (time scale 10-100
>ns). This potential value was taken to increase the impact of NMR
>restraints in total energy. Is this a high potential wall problem
>(atom's movement algorithm under high potential/force) or something else?

It sounds like a problem with the NOESY restraints. You could try some
tests: run DNA with no NMR restraints (should be fine at 300K, based on
tons of experience); use NOE distance restraints (if you have them)
rather than NOESY volume restraints (just as a check); try a smaller
NOESY volume weight (again, just as a test.)

There is an old program, makeCHIR_RST, which will create chirality
restraints for tetrahedral carbons that should (help) prevent chirality
flips. It is in AmberTools/src/nmr_aux/prepare_input. Somehow, it is
no longer installed in $AMBERHOME/bin under the new CMake scripts. But
it's just a shell script: copy it to $AMBERHOME/bin and it will show up
in your PATH.

That said, it's also possible that either your restraint weight or the
NOESY volume setup are causing problems. In that case, enforcing
chirality may only serve to hide the problem. Let us know if you
continue to have problems -- it's been decades since I did things like
this, but I may still have some memory. You can check your settings
against those in the $AMBERHOME/test/noesy folder (note the dates on the
files there?).

>igb=1, saltcon=0.1,

I recommend switching to igb=8 for proteins and DNA: see the Reference
Manual for details.

>ntt=2, temp0=300.0,

I recommend ntt=3 for GB calculations

>&wt type='NOESY', istep1=0,istep2=200000,value1=35.0,

35 does seem like a very high weight, but my memory is fuzzy here.


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Received on Thu Nov 12 2020 - 05:30:03 PST
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