Dear AMBER users,
I am running a membrane protein–peptide ligand simulation using AMBER22
pmemd.cuda with the CHARMM36 force field.
System details:
* Protein residues: 1–325
* Peptide ligand residues: 326–331
* Lipid bilayer system
* NPT semi-isotropic simulation (ntp=3)
* Temperature: 310 K
* dt = 0.002 ps
* barostat=2
* iwrap=0
I am applying positional restraints using the AMBER group restraint
format. *The
restraint groups cover residues 1–331 with a force constant of 10
kcal/mol/Ų.*
Example:
Protein posres1
10.0
FIND
C * * *
CA * * *
CB * * *
...
SEARCH
RES 1 331
END
The mdout file indicates that the restraints are being applied correctly.
For example:
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
and the output also reports a nonzero restraint energy:
RESTRAINT = 2117 kcal/mol
*However, during the trajectory, the peptide ligand and receptor appear to
move significantly relative to each other.*
*I would like to ask whether this behavior is expected for harmonic
positional restraints, or whether it may indicate another issue.*
*My questions are:*
1. Is noticeable peptide motion still expected with 10 kcal/mol/Ų
positional restraints?
2. Could this mainly be a PBC/imaging artifact?
3. For membrane protein–peptide systems, is there a recommended restraint
strategy to better maintain the peptide orientation/position during
equilibration?
Thank you very much for your time and suggestions.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 11 2026 - 04:30:02 PDT
