Dear Jason
Thank you very much for your help. I tried to use your "correct input", but
it still does not work.
Previously, I tried to use only ntr or nmropt options, and it works.
I hope that the problem is the coexistence of both options, but with pmemd
of AMBER9 it seems not to work, but I need to use both restraints, but now
I have any idea how to do
Thank you very much
Elisa
2012/4/1 Jason Swails <jason.swails.gmail.com>
> Hello,
>
> There are still a number of issues with your input file (for example, a
> non-existent namelist is terminated, you moved the &ewald namelist to
> the bottom, but it's not terminated, and DUMPFREQ is _still_ not in
> quotes)
>
> This is a complex combination of input parameters. My suggestion is to
> start with something easier -- the Amber manual, the tutorials, and the
> test cases in $AMBERHOME/test are good starting points. This way, you
> can experiment with more complex options one at a time (keep adding
> something new to the input file to make sure you know what is
> happening). Speaking from experience, you learn much more through trial
> and error (with the aid of the tutorials and manual) than you do from
> someone providing an answer each step of the way.
>
> This should help give you a better understanding of Amber inputs which
> will allow you to diagnose this issues quickly on your own in the
> future.
>
> Good luck,
> Jason
>
> P.S. For reference, I believe this is the 'correct' input file
> ('correct' in that I think it will now run):
>
> run: MD
> &cntrl
> imin = 0, irest = 0 , ntx = 1,
> nstlim = 2500000, dt = 0.002,
> ntc = 2 , ntf = 2,
> ntt = 3, gamma_ln = 2.0,
> tempi = 298.0, temp0 =298.0,
> ntb = 1 ,
> ntpr = 250 , ntwx = 250, ntwr = 500 ,
> cut = 9,
> ig = -1
> ioutfm = 1
> nmropt=1,
> ntr=1
> /
> &ewald
> nfft1 = 90,
> nfft2 = 90,
> nfft3 = 90,
> /
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
> &wt type='DUMPFREQ', istep1=1, /
> &wt type='END' /
> DISANG=dist_chi.RST
> DUMPAVE=restraint.log
> LISTIN=POUT
> LISTOUT=POUT
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Sun Apr 01 2012 - 12:30:02 PDT
