Try setting ntpr=1 and ntwx=1 and see if you ever go beyond the first
step and what happens.
Right now you have them set to 5000, so lots of things could have
happened between those steps.
adrian
On 7/20/17 9:05 AM, Alonso Martinez, Diego wrote:
> 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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Jul 20 2017 - 06:30:03 PDT
