Dear All
I need to perform molecular dynamics simulations with Amber on protein-DNA
complexes which contain Mg ions. The complexes have four protein chains
and two DNA chains, while in the manual for MCPB.py in Amber 22 it is
specified that "original_pdb This is the file name of the original PDB
file, which should have only one chain.".
Please kindly advice how/which tool I can use to prepare for molecular
dynamics a protein-DNA complex containing more than one protein and DNA
chains.
Than you in advance
Iglika Lessigairska, PhD,
IBPBME, Bulgarian Academy of Sciences
Sofia, Bulgaria
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Received on Mon Jan 13 2025 - 03:30:02 PST
