Dear Amber Community,
Following the lysozyme tutorial on thermodynamic integration for mutating a sidechain, TiMerge in ParmEd does not work if I issue
tiMerge :1-162 :163-324 :99&!.1563,1564,1565,1566,1571,1572 :261&!.4166,4167,4168,4169,4174,4175
Where copy #1 of the protein is :1-162, copy #2 is 163-324, and the softcore regions are :99 and :261, but excluding the backbone atoms of each.
The error message is: TiMergeError: The number of nonsoftcore atoms in mol1mask and mol2mask must be the same.
But that is simply not true. Only the sidechains of :99 and :261 change and that is what the above masks select. The total number of atoms for the non-softcore regions is 2603 in both cases.
I really need help with this issue. Otherwise, I’m going to have to abandon using Amber for my next research endeavors, and I don’t want to have to do that.
Tutorial referenced above: https://ambermd.org/tutorials/advanced/tutorial9/index.html#sidechain_mini <https://ambermd.org/tutorials/advanced/tutorial9/index.html#sidechain_mini>
Best,
Matthew
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 18 2022 - 08:00:13 PDT
