Dear Amber users,
I am trying to obtain a MD trajectory of a DNA-protein-metal-ligand complex.
To prepare the inpcrd and prmtop files, I followed the following approach: first, I’ve prepared PDB files of each of the elements of the simulation: the protein and the DNA with the H++ webserver, the ligand and metal with antechamber. Then, I joined all the pdb files into one with the cat command, to then generate the inpcrd and prmtop files of the complex with tleap.
The tleap input file was as follows:
source leaprc.protein.ff14SB
source leaprc.DNA.OL15
source leaprc.water.tip3p
source leaprc.gaff2
CPF = loadmol2 CPF.mol2
loadamberparams CPF.frcmod
loadamberparams frcmod.ions234lm_126_tip3p
mol = loadpdb Gyrase_complex_fixed.pdb
savepdb mol Gyrase_complex_dry.pdb
saveamberparm mol Gyrase_complex_dry.prmtop Gyrase_complex_dry.inpcrd
solvateoct mol TIP3PBOX 15.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol Gyrase_complex_solv.pdb
saveamberparm mol Gyrase_complex_solv.prmtop Gyrase_complex_solv.inpcrd
quit
The method used to parametrize the metal ion is the nonbonded model as we want to observe if the metal ion exits the binding site upon mutations in the protein. The parametrization was checked with parmed.
Inpcrd and prmtop files of the solvated complex were then generated. Then, we proceeded with an energy minimization using sander.MPI, followed by heating with sander.MPI as well. The minimization run fine, at least when compared to previously successful minimizations. However, when it passed to the heating, the mdout file only prints the first step and does not continue the simulation after that, not even generating a trajectory file. The mdout file was:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -393779.1731 EKtot = 0.0000 EPtot = -393779.1731
BOND = 23619.4348 ANGLE = 5814.7119 DIHED = 11047.5656
1-4 NB = 4193.6173 1-4 EEL = 25963.2849 VDWAALS = 29449.7359
EELEC = -493867.5237 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.7721E-03
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
After which no more steps are printed. The program just exits and doesn’t generate trajectory or restart files to continue to the next heating step. The heating input file was:
&cntrl
imin=0,
irest=0,
ntx=1,
nstlim=250000, dt=0.002,
ntc=2, ntf=2,
tol=0.0000001,
cut=10.0, ntb=1,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=1.0,
ig=-1,
ntr=1,
ntp=0,
ioutfm=1,
nmropt=1,
ntxo=2,
/
&wt TYPE='TEMP0', istep1=0, istep2=250000,
value1=0.0, value2=100.0 /
&wt TYPE='END' /
Hold protein and ligand fixed
10.0
RES 1 857
END
END
I’ve tried fixing this issue by removing the energy constraints and changing sander for pmemd but none of these options work. Could you please let me know if you had any issue like this and if so propose possible solutions? Many thanks for your help.
Best wishes,
Diego
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Received on Thu Jul 20 2017 - 06:30:02 PDT
