I’ve run independent trajectories of subunits A and B of a homodimeric protein each of which is in complex with a ligand and a conserved water molecule (named HOH in the topology file) as shown below.
subA-LIG-HOH
subB-LIG-HOH
Both systems are solvated. Due to oversight the order of LIG and HOH in the complex is reversed: subA-HOH-LIG-subB-HOH-LIG
Trying to run MMGBSA following the multi-trajectory approach, I get the following error message
PrmtopError: Couldn't predict mask from topology files!
Your ligand residues must be sequential in your complex.
There are likely problems with your topology files if this is not the case.
My question is whether it is possible to modify the topology and trajectory of the complex (or subA/subB) to get around this problem.
Thanks in advance for any suggestions
George
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Received on Sun Sep 17 2017 - 08:30:02 PDT
