Re: [AMBER] rfree: Error decoding variable 1 3 from:

From: Niel Henriksen <niel.henriksen.utah.edu>
Date: Sun, 1 Apr 2012 21:03:35 +0000

Elisa,

I seem to remember older versions of pmemd being finicky about the order
of options you are using. Try the following modification:

...
...
...
&ewald
nfft1 = 90,
nfft2 = 90,
nfft3 = 90,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END' /
DISANG=dist_chi.RST
DUMPAVE=restraint.log
LISTIN=POUT
LISTOUT=POUT
&end
Keep DNA fixed with weak restraints
0.05
RES 1 48
END
END


I'm not sure, but that may fix your problem.

--Niel

________________________________________
From: Elisa Frezza [elisa.frezza.gmail.com]
Sent: Sunday, April 01, 2012 2:28 PM
To: jason.swails.gmail.com; AMBER Mailing List
Subject: Re: [AMBER] rfree: Error decoding variable 1 3 from:

Dear Jason

I would like to ask you another question, is it possible to use nmropt=1
and ntr=1 with pmemd? Because my problem arise using pmemd.

Thanks

Elisa

2012/4/1 Elisa Frezza <elisa.frezza.gmail.com>

> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Elisa Frezza
> Ph.D. Student in Materials Science and Engineering
> Dipartimento di Scienze Chimiche
> UniversitÓ 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
>
>
>
>


--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
UniversitÓ 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 - 14:30:03 PDT
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