[AMBER] MD with emap restraints, restraints have no effect

From: Will Gerrard <will.gerrard.kuano.ai>
Date: Sat, 3 Jul 2021 10:51:42 +0100


I am attempting to run a short MD simulation where the position of a serine
residue and a ligand are constrained in order to force them into a
conformation obtained from a different structure. The coordinates in the
restraint are a small distance from the starting coordinates in the
simulation, but the restraints seem to have absolutely no effect, even with
very high force constant.

I am hoping this is a simple issue with my input file, but i can't seem to
fix it, any advice would be greatly appreciated,



Here is the sander input file i am using:

MD with only ntr restraint on atoms outside sphere
 imin=0, irest=1, !(imin=0, run md with no minimisation, irest=1,
restart simulation using velocities from input file)
 ntx=5, !(ntx=5, read coordinates and velocities from
coordinate file (NetCDF))
 nstlim=100000, dt=0.001, !(nstlim=500, perform 500 MD steps, dt=0.001
use time step of 0.001 psec)
 ntpr=100, !(print energy every n step)
 ntwx=100, !(write coordinates to crd file every n step)
 ioutfm=1, !(write traj file as formatted ASCII (1 for
 ntwr=10, !(write restart file every 10 steps (set to
negative to write to separate files))
 ntc = 2, tol = 0.0000005, !(use shake to constrain hydrogen bonds only,
with tolerance 0.0000005)
 ntb=0, cut=10, !(no periodic boundary, nonbonded cutoff of 10)
 iemap=1, !(use emap)
 ntt=1, tautp=4.0, temp0=300.0, !(ntt=1 use constant temperature (of temp0)
using weak-coupling algorithm, using tautp time constant for heat bath
coupling, )
 mapfile='../minimize/Protein_lig_solvated.pdb', atmask="!.H= & :356",
!(constrain residue 356 (SER) to coordinates where it connects to Lig)
 fcons=1000000, !(use force constant
 mapfile='../minimize/Protein_lig_solvated.pdb', atmask="!.H= & :364",
!(constrain residue 364 (Lig) to coordinates where it connects to SER)
 fcons=1000000, !(use force constant
AMBER mailing list
Received on Sat Jul 03 2021 - 03:00:02 PDT
Custom Search