On Thu, May 02, 2024, Pietro Aronica wrote:
>Dear all,
Please send amber-related questions to the mail reflector, amber.ambermd.org,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See
http://lists.ambermd.org/mailman/listinfo/amber for information on how to
subscribe.
>When I save a pdb in cpptraj, it will only use 4 columns for the residue
>number, so residue 9999 will be followed by residue 0, then 1, and so
>on. However, leap will use 5 columns, so residue 9999 is followed by 10000,
>10001 and so on. It seems to me that the pdb file format is perfectly happy
>with 5 columns for the residue number, so is there a way to have cpptraj
>also output its pdb in the same manner as leap does, to avoid mismatches
>and bugs?
The (increasing obsolete) PDB format does not allow for more than 10,000
residues. There are a variety of non-standard workarounds, two of which you
see in various parts of Amber.
Amber's internal residue number is incremented by one for each new residue,
and need not correspond to what is in columns 23-26 of a PDB file. Amber
also pretty much ignores chainID's (column 22). So what tleap prints out
may be "perfectly happy" inside Amber, many other programs will interpret
the leading digit of a 5-character residue number as a chainID.
You, of course, are free to do what you want here. What is output by
cpptraj can be used in many other programs, but no single workaround can be
relied upon. If you really want five-character residue numbers, just load your
current coordinates into tleap, and run savePdb from there. Or, you could
write a little script to convert what cpptraj puts out into something more
to your liking.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 03 2024 - 09:30:02 PDT
