Dear David and Anselm
I think I will try out both the suggestions once I figure out the solution
to my other question that is on a different mail thread: parameter
generation for noncanonical residues. I will get back to you.
just a quick question to Anselm, what is this combine command in tleap?
Sorry, I could not find this and would really appreciate a help with the
syntax. I am using Amber 20
Thanks
Suchetana
On Fri, Nov 11, 2022 at 8:25 AM David A Case <david.case.rutgers.edu> wrote:
> 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 - 09:30:03 PST
