On Thu, Nov 10, 2022, Suchetana Gupta via AMBER wrote:
>I am trying to simulate a protein-cyclic peptide complex and have a basic
>question.
>
>My question is, when I simulate the peptide-protein complex, how do I frame
>the leap input file? I am concerned about the loadPDB part.
Here's what I always do. It's not necessarily the best way, but to me, it
seems simplest.
Make a single PDB file with both the protein and the peptide, separated by a
TER card. Then in your leap.in file, load all necessary libraries and
frcmod files. Then use a single loadPdb file (not loadPdbusingseq) to
get a unit that has everything you want. Use the bond command to add the
missing "cyclic" bond for the peptide. (Use the "desc" command first to see
which residue numbers correspond to the peptide).
Then you can continue with solvate commands, etc. If tleap reports an
error, try to see if you can fix it.
To me (maybe not to others) it seems simpler to use a text editor to create
a starting PDB file that has everything I want than to bother with several
loadPdb commands and try to grok how combine these later inside tleap.
....good luck...dac
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Received on Fri Nov 11 2022 - 09:00:03 PST
