Best to copy/paste actual output.
Residues get numbered sequentially when leap builds a model, and pdb
residue numbers are lost.
One way to see the new residue numbers is to savepdb in leap, so you
have a pdb to go from.
Bill
On 7/4/17 8:00 AM, NADIA RAHMAH wrote:
> Hello. I run MD for protein complex docked, in complex pdb file
> (preparation result), there are 292 residu number, which 1-291 are protein
> (receptor) amino acid residue and residue number 292 is the ligand name
> UNL. When I run preparation solvated box and without no box, there are
> written like:
> there is bond 297 <UNL> <Br>
> There is bond 297 <UNL> <H>
>
> It written UNL in 297 residu. I confuse how Amber read my protein residue
> number? How I can see the list of all residue number, I have to know what
> is residue number of the ligand, I need to fix it because I want analyst it
> with RMSD, MMPBSA, etc.
> I hope anybody can help me. Thanks
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Received on Tue Jul 04 2017 - 09:00:03 PDT
