Dear all,
I am currently trying to run an MD simulation of an RNA molecule stabilized
by several Mg2+ ions using the AMBER16 package.
I need to parametrize the metal coordination centers in order to avoid the
Mg2+ leaving their original sites. I tried MCPB as I already used it for
metalloenzymes. However, the system the first MCPB step created does not
cap the nucleotides as it would do with the amino acids in order to do the
QM calculations (Gaussian) as it leaves opened valences. I decided to
manually cap the nucleotides and generate Gaussian input files so that the
charge calculation would be correct, but now that I want to run the second
MCPB step I’m facing a discrepancy between mi QM outputs and the
*standard.fingerprint files produced in the first step. And if I try to run
the first MCPB step using PDBs with the caped nucleotides, the program
doesn’t seem to understand the molecules I’m giving it.
Can anyone give me a bit of insight on how to tackle this issue? Is there
another version of MCPB that allows the parametrization I’m trying to do?
Claire
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Received on Wed Sep 02 2020 - 03:00:02 PDT
