Dear Gupta,
I suspect that LeaP didn't create one cyclic structure to follow your
commands. When you use the sequence command the LEap creates one strand
structure. Then I could suggest you run some windows of Umbrella Sampling
(use restraint) to approximate the extreme to a good distance. Then save
the PDB, load on the LEap, and create this bond as you did before.
Best,
Carol
On Thu, Nov 10, 2022, 6:03 PM Suchetana Gupta via AMBER <amber.ambermd.org>
wrote:
> 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 - 18:00:03 PST
