On Thu, Feb 04, 2010, Hopkins, Robert wrote:
>
> I'm using AmberTools-1.3 in a Cygwin environment. After I created
> several PDB files in ptraj, I then loaded each of them into xleap for
> further processing. The leap.log in each case indicates that *none* of
> the residues (e.g., DC5, DG, Na+, WAT, etc.) was recognized by xleap (or
> by tleap when I tried that), yet the functioning of either leap program
> appeared to be fine otherwise. An example leap.log file is attached.
If you are concerned by messages of this sort:
(Residue 22: DC, Nonterminal, was not found in name map.)
you may ignore them. It just means that the input name was not being mapped
(via PdbResMap) to another name. This is only printed a "maximum verbosity"
but probably is never needed.
Amber developers: does anyone see a reason why this should not be commented
out for the next release? Actual mapping is logged, but the default behavior
of issuing the above message on no-mapping seems to just create "noise".
[To partially answer my own question: it does log that the residue has been
read, mapped or not; so I could see it possible being useful in some debugging
situations. But I've never used it this way in 20 years....]
....dac
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Received on Thu Feb 04 2010 - 19:30:03 PST
