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
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
_______________________________________________
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 Thu Apr 05 2012 - 08:00:07 PDT
