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

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Thu, 29 Mar 2012 15:46:30 +0200

Hello

Thank you for your answer. If I remove "&end" and " / ", the error will not
disappear.
I tried to write the following input, and it is ok, but I would like to ask
you a question: is it correct that in output file there is not reported the
fact that there are the restraints for DNA RES 1 48 (part 5)?

thank you in advance

ELisa

----------------------------
Input file:

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


-------------
Part of output file

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 9

| Run on 03/29/2012 at 15:41:22

  [-O]verwriting output

File Assignments:
| MDIN: run_md.in

| MDOUT: dimero_water_SCP_md.out

| INPCRD: dimero_water_SPC.inpcrd

| PARM: dimero_water_SPC.prmtop

| RESTRT: dimero_water_SPC_md.rst

| REFC: dimero_water_SPC.inpcrd

| MDVEL: mdvel

| MDEN: dimero_water_SPC_md.en

| MDCRD: dimero_water_SPC_md.mdcrd

| MDINFO: mdinfo

|LOGFILE: logfile



 Here is the input file:

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,

 /

 &ewald

 nfft1 = 90,

 nfft2 = 90,

 nfft3 = 90

/

&end

&wt type=DUMPFREQ, istep1=1, /

&wt type=END &end

DISANG=dist_chi.RST

DUMPAVE=restraint.log

LISTIN=POUT

LISTOUT=POUT

Keep DNA fixed with weak restraints

0.05

RES 1 48

END

END





| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| FFTW_FFT
| FFTLOADBAL_2PROC
| BINTRAJ
| MKL

| Largest sphere to fit in unit cell has radius = 35.598

| New format PARM file being parsed.
| Version = 1.000 Date = 09/30/11 Time = 16:42:41
| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

 getting new box info from bottom of inpcrd

 NATOM = 43314 NTYPES = 19 NBONH = 42238 MBONA = 1088
 NTHETH = 1280 MTHETA = 1672 NPHIH = 2588 MPHIA = 3040
 NHPARM = 0 NPARM = 0 NNB = 64116 NRES = 14050
 NBONA = 1088 NTHETA = 1672 NPHIA = 3040 NUMBND = 43
 NUMANG = 86 NPTRA = 48 NATYP = 30 NPHB = 1
 IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Coordinate Index Table dimensions: 15 15 15
| Direct force subcell size = 5.8131 5.8131 5.8131

     BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------




General flags:
     imin = 0, nmropt = 1

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 250, ntrx = 1, ntwr =
500
     iwrap = 0, ntwx = 250, ntwv = 0, ntwe =
  0
     ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
   0

Potential function:
     ntf = 2, ntb = 1, igb = 0, nsnb =
 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Molecular dynamics:
     nstlim = 2500000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Langevin dynamics temperature regulation:
     ig = -1
     temp0 = 298.00000, tempi = 298.00000, gamma_ln= 2.00000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

NMR refinement options:
     iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
  1
     scalm = 100.00000, pencut = 0.10000, tausw = 0.10000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme =
  1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 87.197 Box Y = 87.197 Box Z = 87.197
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 90 NFFT2 = 90 NFFT3 = 90
     Cutoff= 9.000 Tol =0.100E-04
     Ewald Coefficient = 0.30768
     Interpolation order = 4

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------



 begin time read from input coords = 0.000 ps



           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 DUMPFREQ 1 0 0.000000 0.000000 0 0
                         ** No weight changes given **

 RESTRAINTS:
 Requested file redirections:
  DISANG = dist_chi.RST
  DUMPAVE = restraint.log
  LISTIN = POUT
  LISTOUT = POUT
 Restraints will be read from file: dist_chi.RST
Here are comments from the DISANG input file:

******
 COM ( -1)-COM ( -1) NSTEP1= 1
NSTEP2=100000
 Atom ranges defining first Center of Mass Group:
   157 -> 161/ 164 -> 164/ 166 -> 167/ 169 -> 170/ 172 ->
175/
   178 -> 179/ 181 -> 183/ 185 -> 185/ 188 -> 193/ 196 ->
196/
   198 -> 199/ 201 -> 202/ 204 -> 205/ 209 -> 211/ 213 ->
215/
   217 -> 217/ 220 -> 220/ 536 -> 540/ 543 -> 543/ 545 ->
546/
   548 -> 549/ 551 -> 554/ 557 -> 558/ 560 -> 562/ 564 ->
564/
   567 -> 572/ 575 -> 575/ 577 -> 578/ 580 -> 581/ 583 ->
584/
   588 -> 590/ 594 -> 594/ 596 -> 596/ 599 -> 599/
 Atom ranges defining second Center of Mass Group:
   915 -> 919/ 922 -> 922/ 924 -> 925/ 927 -> 928/ 930 ->
933/
   936 -> 937/ 940 -> 941/ 943 -> 943/ 946 -> 951/ 954 ->
954/
   956 -> 957/ 959 -> 960/ 962 -> 963/ 967 -> 969/ 971 ->
973/
   975 -> 975/ 978 -> 978/ 1294 -> 1298/ 1301 -> 1301/ 1303 ->
 1304/
  1306 -> 1307/ 1309 -> 1312/ 1315 -> 1316/ 1319 -> 1320/ 1322 ->
 1322/
  1325 -> 1330/ 1333 -> 1333/ 1335 -> 1336/ 1338 -> 1339/ 1341 ->
 1342/
  1346 -> 1348/ 1350 -> 1352/ 1354 -> 1354/ 1357 -> 1357/
R1 = 0.000 R2 = 18.000 R3 = 18.000 R4 = 100.000 RK2 = 5.000 RK3 =
 5.000
 Rcurr: 23.030 Rcurr-(R2+R3)/2: 5.030 MIN(Rcurr-R2,Rcurr-R3):
 5.030
                       Number of restraints read = 1

                  Done reading weight changes/NMR restraints


 Number of triangulated 3-point waters found: 13898

     Sum of charges from parm topology file = -0.00001498
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals 1459974
| Integers 1141225

| Nonbonded Pairs Initial Allocation: 818837

| Running AMBER/MPI version on 16 nodes


--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------






2012/3/29 Jason Swails <jason.swails.gmail.com>

> Hello,
>
> On Thu, 2012-03-29 at 15:04 +0200, Elisa Frezza wrote:
> > Dear all
> >
> > I use amber 9 and I would like to use pmemd.
> > I'll report my input file and I hope that someone may help me.
> > The error is :
> >
> >
> > rfree: Error decoding variable 1 3 from:
> > DUMPAVE=restraint.log
>
> rfree is the subroutine that parses the group-style input (stands for
> free-format input). This suggests that pmemd is thinking that your
> restraint file specifications are part of the group input.
>
> > 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
> > ntr = 1
> > nmropt=1,
> > /
> > &ewald
> > nfft1 = 90,
> > nfft2 = 90,
> > nfft3 = 90
> > /
> > &end
>
> This &end should not be here.
>
> > Keep DNA fixed with weak restraints
> > 0.05
> > RES 1 48
> > END
> > END
> > /
>
> Neither should this /
>
> Here is what is happening (I think): the input file parser thinks it has
> found a "&end" namelist that you've defined. However, no part of your
> simulation demands a &end namelist, so it is not read, but it's also not
> tagged as the group input section (which is what it is). Therefore, the
> parser tries to parse the part of the input file below as the GROUP
> input for the restraints.
>
> Long story short, remove the &end and / that I tagged above, and it
> should win.
>
> HTH,
> Jason
>
> --
> 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
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Received on Thu Mar 29 2012 - 07:00:04 PDT
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