Dear Amber Users
I am trying to simulate a protein-cyclic peptide complex and have a basic
question.
When I simulated the cyclic peptide only, the leap.in file had the lines
like:
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams xyz.frcmod
loadamberparams abc.frcmod
loadoff xyz.lib
loadoff abc.lib
seq = { A B C D E F G }
cycpep = loadPDBusingseq peptide.pdb seq
bond cycpep.1.N cycpep.8.C
solvatebox cycpep TIP3PBOX 15.0
check cycpep
charge cycpep
addions cycpep Na+ 0
addions cycpep Cl- 0
savepdb cycpep peptide_wat_out.pdb
saveAmberParm cycpep peptide_wat.top peptide_wat.crd
quit
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. How do I load
the PDB file of the complex while also taking care that the cyclic bond
remains intact? The complex PDB obviously has the cyclic bond intact. (I am
asking because when I did not use the loadPDBusingseq function while
simulating the peptide only, despite starting with an intact cyclic
peptide, the bond did not remain in the simulation)
Can someone please help me with this?
Thanks
Suchetana
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Received on Thu Nov 10 2022 - 17:30:02 PST
