AMBER Archive (2005)

Subject: AMBER: Trouble with example tutorial

From: Maciej (makay22_at_wp.pl)
Date: Wed May 11 2005 - 06:08:02 CDT

I try to make example turorial

"Thermodynamic integration calculations using sander

Running the charging calculation in vacuum"

Amd I have that errors

 

 

 

 

$AMBERHOME/exe/sander -O -i md.in -o eq2.o -c eq1.x -p prmtop.coul.vac -r eq2.x

forrtl: No such file or directory

forrtl: severe (29): file not found, unit 9, file /home/obliczenia/amber8/obliczenia/kasia/PHE/fort.9

Image PC Routine Line Source

sander 08205804 Unknown Unknown Unknown

 

Stack trace terminated abnormally.

 

 

 

 

          -------------------------------------------------------

          Amber 8 SANDER Scripps/UCSF 2004

          -------------------------------------------------------

 

| Run on 05/11/2005 at 11:32:04

  [-O]verwriting output

 

File Assignments:

| MDIN: md.in

| MDOUT: eq2.o

|INPCRD: eq1.x

| PARM: prmtop.coul.vac

|RESTRT: eq2.x

| REFC: refc

| MDVEL: mdvel

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

 

 

 Here is the input file:

 

neutralize toluene

 &cntrl

  ntr = 0,

  nstlim = 100000, nscm = 2000, ntave = 10000,

  ntx = 5, irest = 1, ntb = 0, ntpr = 200,

  dt = 0.001, nrespa = 2,

  ntt = 1, temp0 = 300., tautp = 2.0,

  ntc = 2, ntf = 2, tol = 0.000001,

  ntwr = 10000, ntwx = 0,

  icfe = 1, clambda = 0.5,

 &end

 

--------------------------------------------------------------------------------

   1. RESOURCE USE:

--------------------------------------------------------------------------------

 

| Flags: MPI

| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation

 

 

 

 

 

When i change parameters

 

          -------------------------------------------------------

          Amber 8 SANDER Scripps/UCSF 2004

          -------------------------------------------------------

 

| Run on 05/11/2005 at 11:21:26

  [-O]verwriting output

 

File Assignments:

| MDIN: md.in

| MDOUT: eq2.o

|INPCRD: eq1.x

| PARM: prmtop.coul.vac

|RESTRT: eq2.x

| REFC: refc

| MDVEL: mdvel

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

 

 

 Here is the input file:

 

neutralize toluene

 &cntrl

  ntr = 0,

  nstlim = 100000, nscm = 2000, ntave = 10000,

  ntx = 5, irest = 1, ntb = 0, ntpr = 200,

  dt = 0.001, nrespa = 2,

  ntt = 1, temp0 = 300., tautp = 2.0,

  ntc = 2, ntf = 2, tol = 0.000001,

  ntwr = 10000, ntwx = 0,

  icfe = 1, clambda = 0.5,

  cut = 8.1,

  igb = 1,

 &end

 

--------------------------------------------------------------------------------

   1. RESOURCE USE:

--------------------------------------------------------------------------------

 

| Flags: MPI

| New format PARM file being parsed.

| Version = 1.000 Date = 04/27/05 Time = 11:01:19

 NATOM = 15 NTYPES = 4 NBONH = 8 MBONA = 7

 NTHETH = 16 MTHETA = 8 NPHIH = 27 MPHIA = 9

 NHPARM = 0 NPARM = 0 NNB = 68 NRES = 1

 NBONA = 7 NTHETA = 8 NPHIA = 9 NUMBND = 4

 NUMANG = 5 NPTRA = 3 NATYP = 4 NPHB = 0

 IFBOX = 0 NMXRS = 15 IFCAP = 0 NEXTRA = 0

 NCOPY = 0

 

 

| Memory Use Allocated

| Real 566

| Hollerith 93

| Integer 20674

| Max Pairs 1

| Max Rstack 46

| Max Istack 1

| Total 85 kbytes

 

Running a free energy calculation with lambda = 0.500

| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

 

--------------------------------------------------------------------------------

   2. CONTROL DATA FOR THE RUN

--------------------------------------------------------------------------------

 

PHE

 

General flags:

     imin = 0, nmropt = 0

 

Nature and format of input:

     ntx = 5, irest = 1, ntrx = 1

 

Nature and format of output:

     ntxo = 1, ntpr = 200, ntrx = 1, ntwr = 10000

     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0

     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

 

Potential function:

     ntf = 2, ntb = 0, igb = 1, nsnb = 25

     ipol = 0, gbsa = 0, iesp = 0

     dielc = 1.00000, cut = 8.10000, intdiel = 1.00000

     saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000

     gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500

     rdt = 0.00000, rgbmax = 25.00000

     scnb = 2.00000, scee = 1.20000

 

Frozen or restrained atoms:

     ibelly = 0, ntr = 0

 

Molecular dynamics:

     nstlim = 100000, nscm = 2000, nrespa = 2

     t = 0.00000, dt = 0.00100, vlimit = 20.00000

 

Berendsen (weak-coupling) temperature regulation:

     temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000

 

SHAKE:

     ntc = 2, jfastw = 0

     tol = 0.00000

 

Free energy options:

     klambda = 1

     clambda = 0.50000

 

--------------------------------------------------------------------------------

   3. ATOMIC COORDINATES AND VELOCITIES

--------------------------------------------------------------------------------

 

 

  Unit 9 Error on OPEN: eq1.x

 

 

 

Where from that file eq1.x gets ?????????????

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