On Fri, May 10, 2024, Abdelrahman, Noureen via AMBER wrote:
>
>I am trying to produce the parameters and coordinates files for this
>pdb (attached here). Please note that the two chains are separated by
>TER lines: one between the two chains and one at the end. They also
>have different chain identifiers. When I visualize the pdb in VMD, the
>two chains are distinguishable (colored differently). However, when
>I run tleap (code attached below), then visualize the parameters and
>coordinates files produced from tleap (were too big to attach here but
>can be reproduced using the attached pdb and tleap files), the chains are
>indistinguishable. Can someone please let me know if I'm missing something
>here?
For historical reasons (mainly that the original Amber codes were written
before simulations on multichain proteins were commonplace) Amber doesn't
make any use of chainIDs. If look look at apo_smurfp.pdb with a text editor
(and not just with VMD) you will see what is going on.
In Amber, each new residue gets a number one bigger than the preceeding one,
and the chainID column is not populated. If you wish the two chains to have
different colors in a visualization program like VMD, you will have to enter
commands in VMD to make that happen.
More recently, Amber has a partial solution to these issues. You can use
the "savePdb" action in parmed to store the "original" residue numbers and
chainID's (and other info) into the prmtop file. Amber will still ignore
these during a simulation. But afterwards, you can use ambpdb from cpptraj
to create PDB files that restore the information contained in the prmtop
file. And, there are options in cpptraj to use the "original" PDB scheme
for most analysis tasks as well. (You have to use ambpdb to get this
behavior; the savePdb command in tleap doesn't have this option.)
...hope this helps...dac
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Received on Fri May 10 2024 - 15:30:03 PDT
