I gave that a try and I still didn’t get any outputs; however, I think it is an issue with connecting my laptop to the computer I am running the simulation on since a shorter version of the simulation ran to completion and provided me with output files when I ran it directly. Thank you for the help.
Thanks,
Chase
> On Jan 26, 2017, at 6:51 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 27 2017 - 18:00:03 PST
