Try setting ntpr=1 to see if you can isolate what is going wrong.
On Thu, Jan 26, 2017 at 3:29 PM, Chase Zagorec-Marks <
chasezgrcmrks.gmail.com> wrote:
> Hello,
>
> I have been trying to perform an implicit solvent constant pH molecular
> dynamics simulation of an eleven residue polypeptide chain at pH = 5, but I
> have been having difficulties with performing the heating portion of the
> simulation. The problem that keeps happening is that the heating will end
> after a few seconds and no output files will be generated. I think the
> issue is either with my parameter and topology file or the .rst file that
> was produced during the initial minimization because I have attempted to
> use previous heating input files- which have worked in the past for other
> structures- and these files have also had the same issue. Below are the
> commands and input files I used to minimize the chain. Is there somewhere
> that I skipped a step or made an error in the input files? Thanks for all
> the help.
>
> Thanks,
> Chase Zagorec-Marks
>
>
> Commands:
>
> pdb4amber -i 11-mer_pH.pdb —constantph -o 11-mer_pH_2.pdb
>
> xleap
>
> source leaprc.constph
>
> x = loadpdb 11-mer_pH_2.pdb
>
> check x
>
> This returned:
> Checking 'x'....
> WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
> Checking parameters for unit 'x'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 1
> Unit is OK.
>
> saveamberparm x 11-mer_pH.parm7 11-mer_pH.inpcrd
> saveamberparm x 11-mer_pH.parm7 11-mer_pH.rst7
>
> Note: When viewed in vmd the structure looked fine for .parm7 and .rst7,
> but when viewed in vmd the chain has the nitrogen of the n-terminal
> extending far from the rest of the chain for the .inpcrd file.
>
> exit xleap
>
> cpinutil.py -p 11_mer_pH.parm7 -resnames HIP GL4 AS4 -o 11_mer_pH.cpin
>
> Min.in file:
>
> Minimization of eleven mer for constant pH MD
> &cntrl
> imin = 1,
> igb = 2,
> saltcon = 0.1,
> maxcyc = 10000,
> ncyc = 1000,
> icnstph = 1,
> ntcnstph = 1000000,
> cut = 1000.0,
> ntr = 1,
> restraint_wt = 10,
> restraintmask = '.CA,C,O,N'
> /
>
> sander.MPI -O -i min.in -o min.mdout -p 11_mer_pH.parm7 -c 11_mer_pH.rst7
> -ref 11_mer_pH.rst7 -r min.rst7 -cpin 11_mer_pH.cpin
>
> Heat.in file:
>
> Implicit solvent constant pH initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=250, ntwx=250, nstlim=2000000,
> dt=0.0005, ntt=3, tempi=10,
> temp0=300, tautp=2, ig=-1,
> ntp=0, ntc=2, ntf=2, cut = 999,
> ntb=0, igb=2, tol=0.000001,
> nrespa=1, saltcon=0.1, icnstph=1,
> solvph=5, ntcnstph=100000000,
> gamma_ln=5.0, ntwr=250, ioutfm=1,
> nmropt=1, ntr=1, restraint_wt=1.0,
> restraintmask='.CA,C,O,N',
> /
> &wt
> TYPE='TEMP0', ISTEP1=1, ISTEP2=1000000,
> VALUE1=10.0, VALUE2=300.0,
> /
> &wt TYPE='END’ /
>
> sander.MPI -O -i heat.in -o heat.mdout -p 11_mer_pH.parm7 -c min.rst7
> -ref min.rst7 -r heat.rst7 -cpin 11_mer_pH.cpin -x heat.mdcrd
>
>
>
>
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>
--
Jason M. Swails
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Received on Thu Jan 26 2017 - 18:00:02 PST
