Dear Amber Users and Developers:
We solvated a system on Xleap that requires many waters. The pdb, prmtop,
and inpcrd files, after residue number 9,999, started numbering the residues
with 1. This caused amino acid residues to have the same residue number as
some water molecules. Same thing happens with atom numbers after 99,999.
Does this cause a problem in our simulations? We think that when using
residue number to place constraints it does. We also are not compfortable
with the idea of two atoms having the same number.
How can this be fixed? Is there a way besides the manually editing of the
pdb file and reloading everything again into Xleap to create new prmtop and
inpcrd files?
Thanks,
David
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Received on Thu Aug 04 2011 - 16:00:02 PDT
