GROMACS version:2024.06
GROMACS modification: Yes/No
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I am adding hydrogen atoms to the complex containing protein, DNA and RNA, and I want to run the MD simulations with the Amber14SB forcefields for protein, OL15 for DNA and OL3 for RNA. Before that, i need to pretreat the structures file. Now i have two ways for that and the questions are as follows:
(1) If i take the pdb2gmx tool to add the hydrogen atoms to the complex, the obtained structure have apparent mistakes (such as the hydrogen atom added to the benzene ring is not coplanar with the benzene ring, which is not reasonable), and after the simulation, even the six carbon atoms of the benzene ring are not in the same plane strictly, i want to know what’s the problem and how can fia that? The mdp settings are below:
;NPT MD
integrator = md
dt = 0.002 ;ps
nsteps = 50000000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstxtcout = 2000
nstcalcenergy = 100
nstenergy = 2000
nstlog = 2000
pbc = xyz
periodic-molecules = no
cutoff-scheme = Verlet
verlet-buffer-tolerance = 0.005
rlist = 1.1
nstlist = 10
vdwtype = Cut-off
vdw-modifier = None
DispCorr = EnerPres
rvdw = 1.0
coulombtype = PME
rcoulomb = 1.0
epsilon-r = 1.0
tcoupl = V-rescale
tc_grps = System
tau_t = 1.0
ref_t = 310
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
constraints = H-bonds
constraint_algorithm = LINCS
continuation = yes
nstcomm = 100
comm_mode = linear
comm_grps = System
(2) If i take other tools to add hydrogen atoms and make structures optimization (such as Phenix and AmberTools), i can get the obviously correct coordinates of hydrogen, but the names of hydrogen atoms added by Phenix were not consistent with the names included in the aminoacids.rtp files of the Amber forcefield files, how to solve that problem?