Elisa,
I think this means that one of your input files has a problem.
If you send me all the input files directly (off the AMBER list)
I will try to troubleshoot.
--Niel
________________________________________
From: Elisa Frezza [elisa.frezza.gmail.com]
Sent: Wednesday, April 11, 2012 8:58 AM
To: AMBER Mailing List
Subject: Re: [AMBER] rfree: Error decoding variable 1 3 from:
Dear Niel,
I put the "&end", but now I have this error:
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
2012/4/11 Niel Henriksen <niel.henriksen.utah.edu>
> Elisa,
>
> I have just now tested a system with almost identical
> setup using pmemd 10. You must have the "&end"
> where I specified:
>
> 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,
> /
> &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
>
> Please copy and paste that directly and try again.
> Reply with any errors. I can confirm that if I remove
> that "&end" I get the same error that you mention.
>
> Good luck,
> --Niel
>
>
> _______________________________________________
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> AMBER.ambermd.org
> 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 Wed Apr 11 2012 - 08:30:03 PDT
