Re: [AMBER] Joining two molecules

From: Daniel Roe <>
Date: Wed, 26 May 2021 09:33:26 -0400


On Wed, May 26, 2021 at 5:17 AM Gustaf Olsson <> wrote:
> bond :1.CB,:1.C2
> Is :1 the now joined molecule? Otherwise, should I provide the correct residue number :2.X,1.X

No, the bond masks are "<tgt>,<src>" - i.e. they are specific to the
molecules *before* you join everything. So in the above case, it means
"bond atom CB in residue 1 of target to atom C2 in residue 1 of
source". The code will internally update indices to keep track of what
is what after atoms are removed. Hopefully this clears it up, let me
know if not


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Received on Wed May 26 2021 - 07:00:02 PDT
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