On Mon, Jun 24, 2019, Akinpelu Olayinka wrote:
>After running Partial and Full minimization for my system of a protein
>and a ligand (GDP) complex, the Heating process is giving the following
>error�
>
>Coordinate resetting (SHAKE) cannot be accomplished,
>
>�� � deviation is too large
>�� � NITER, NIT, LL, I and J are :� � � 0� � � 1 � 2173 � 4302 � 4334
Look at what the geometry is around atoms 4302 and 4334. Are these part
of the GDP? Is either one a hydrogen?
>�� � Note: This is usually a symptom of some deeper
>�� � problem with the energetics of the system.
This means that you need to find the source of the underlying problem--
the SHAKE error is just a symptom, not a cause.
If you system has hydrogens connected to phosphates (e.g. in a
protonated GDP), and if those hydrogens have a zero vdW radius, that is
a common source of problems. But you will need to do some investigation
to see if you localize the problem some.
....dac
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Received on Mon Jun 24 2019 - 09:00:03 PDT
