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

From: Niel Henriksen <niel.henriksen.utah.edu>
Date: Wed, 11 Apr 2012 13:53:03 +0000

I think I have found pmemd v10 to test things on.
Can you send me all your input files?

--Niel

________________________________________
From: Elisa Frezza [elisa.frezza.gmail.com]
Sent: Wednesday, April 11, 2012 2:03 AM
To: AMBER Mailing List
Subject: Re: [AMBER] rfree: Error decoding variable 1 3 from:

Dear Niel

I have tried without &end but I have still error " rfree: Error decoding
variable 1 3 from:"
Thank you for the suggestion, have you any idea how to overcome the new
error?

Thank you very much

ELisa


2012/4/5 Niel Henriksen <niel.henriksen.utah.edu>

> Elisa,
>
> Did you try both formats? ie, with and without
> the "&end" that Jason and I discussed?
>
> Just for the sake of experimentation, you might try
> using "&end" instead of "/" in all cases. That may
> just be a superstition I developed with pmemd in
> amber10 though.
>
> --Niel
> ________________________________________
> From: Elisa Frezza [elisa.frezza.gmail.com]
> Sent: Thursday, April 05, 2012 3:06 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] rfree: Error decoding variable 1 3 from:
>
> Dear Niel
>
> Thank you very much for your suggestion.
> Now I have a new error. It seems that it reads 2 group instead of only one,
> and it does not read NMR constraints.
> Any suggestions?
>
> Thanks
>
> Elisa
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Keep DNA fixed with weak restraints
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 0.05000
> GRP 1 RES 1 TO 48
> Number of atoms in this group = 1516
> ----- READING GROUP 2; TITLE:
> END
>
>
> rfree: End of file on unit 5
>
>
> 2012/4/1 Niel Henriksen <niel.henriksen.utah.edu>
>
> >
> > According to my old input files, you do need the "&end" in the location
> > I specified (for whatever reason).
> >
> > But feel free to try otherwise if it doesn't work.
> >
> > --Niel
> > ________________________________________
> > From: Jason Swails [jason.swails.gmail.com]
> > Sent: Sunday, April 01, 2012 3:04 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] rfree: Error decoding variable 1 3 from:
> >
> > On Sun, Apr 1, 2012 at 5:03 PM, Niel Henriksen <niel.henriksen.utah.edu
> > >wrote:
> >
> > > 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
> > >
> >
> > but no &end here
> >
> > --
> > 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
> >
> > _______________________________________________
> > 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
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> AMBER mailing list
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>



--
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 Wed Apr 11 2012 - 07:00:05 PDT
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