Dear Niel
I use AMBER10 for my calculations.
Thank you
Elisa
The input files are
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
dist_chi.RST:
&rst iat=-1,-1,
ninc=0,ir6=0,ifntyp=0,nstep1=1,nstep2=100000,
r1=0.0000E+00,r2=18.0000,r3=18.0000,r4=100.000,rk2=5,rk3=5,
igr1 =
157,158,159,160,161,164,166,167,169,170,172,173,174,175,178,179,
181,182,183,185,188,189,190,191,192,193,196,198,199,201,202,204,205,209,210,211,
213,214,215,217,220,536,537,538,539,540,543,545,546,548,549,551,552,553,554,557,
558,560,561,562,564,567,568,569,570,571,572,575,577,578,580,581,583,584,588,589,
590,594,596,599,
igr2 =
915,916,917,918,919,922,924,925,927,928,930,931,932,933,936,937,
940,941,943,946,947,948,949,950,951,954,956,957,959,960,962,963,967,968,969,971,
972,973,975,978,1294,1295,1296,1297,1298,1301,1303,1304,1306,1307,1309,1310,1311
,1312,1315,1316,1319,1320,1322,1325,1326,1327,1328,1329,1330,1333,1335,1336,1338
,1339,1341,1342,1346,1347,1348,1350,1351,1352,1354,1357/
2012/4/11 Niel Henriksen <niel.henriksen.utah.edu>
> 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
> > 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
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> > 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
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>
> _______________________________________________
> 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
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Received on Wed Apr 11 2012 - 08:00:04 PDT
