AMBER Archive (2009)

Subject: Re: [Amber]: REMD using hybrid solvent model

From: Morad Mustafa (alawneh_at_uga.edu)
Date: Fri Aug 14 2009 - 07:44:44 CDT

Here is the output of ptraj with its version:
  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
  -/- Executable is: "ptraj"
  /-\
  \-/ Residue labels:
 GLY GLU ALA PRO ASN GLN ALA LEU LEU ARG
 ILE LEU LYS GLU THR GLU PHE LYS LYS ILE
 LYS VAL LEU GLY SER GLY ALA PHE GLY THR
 VAL TYR LYS GLY LEU TRP ILE PRO GLU GLY
 GLU LYS VAL LYS ILE PRO VAL ALA ILE LYS
 GLU LEU ARG GLU ALA THR SER PRO LYS ALA
 ASN LYS GLU ILE LEU ASP GLU ALA TYR VAL
 MET ALA SER VAL ASP ASN PRO HIE VAL CYS
 ARG LEU LEU GLY ILE CYS LEU THR SER THR
 VAL GLN LEU ILE THR GLN LEU MET PRO PHE
 GLY CYS LEU LEU ASP TYR VAL ARG GLU HIE
 LYS ASP ASN ILE GLY SER GLN TYR LEU LEU
 ASN TRP CYS VAL GLN ILE ALA LYS GLY MET
 ASN TYR LEU GLU ASP ARG ARG LEU VAL HIE
 ARG ASP LEU ALA ALA ARG ASN VAL LEU VAL
 LYS THR PRO GLN HIE VAL LYS ILE THR ASP
 PHE GLY LEU ALA LYS LEU LEU GLY ALA GLU
 GLU LYS GLU TYR HIE ALA GLU GLY GLY LYS
 VAL PRO ILE LYS TRP MET ALA LEU GLU SER
 ILE LEU HIE ARG ILE TYR THR HIE GLN SER
 ASP VAL TRP SER TYR GLY VAL THR VAL TRP
 GLU LEU MET THR PHE GLY SER LYS PRO TYR
 ASP GLY ILE PRO ALA SER GLU ILE SER SER
 ILE LEU GLU LYS GLY GLU ARG LEU PRO GLN
 PRO PRO ILE CYS THR ILE ASP VAL TYR MET
 ILE MET VAL LYS CYS TRP MET ILE ASP ALA
 ASP SER ARG PRO LYS PHE ARG GLU LEU ILE
 ILE GLU PHE SER LYS MET ALA ARG ASP PRO
 GLN ARG TYR LEU VAL ILE GLN GLY ASP GLU
 ARG MET HIE LEU PRO SER PRO THR ASP SER
 ASN PHE TYR ARG ALA LEU MET ASP GLU GLU
 ASP MET ASP ASP VAL VAL ASP ALA ASP GLU
 TYR LEU ILE K+ K+ K+ K+ K+ K+ K+
 K+ WAT WAT WAT WAT WAT WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT WAT WAT
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin ../REMD-001.mdcrd remdtraj
  Checking coordinates: ../REMD-001.mdcrd
PTRAJ: trajout REMD-001-Test.mdcrd
PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 500 frames.
       Summary of I/O and actions follows:
INPUT COORDINATE FILES
  File (../REMD-001.mdcrd) is an AMBER trajectory (with box info) with 500 sets
OUTPUT COORDINATE FILE
  File (REMD-001-Test.mdcrd) is an AMBER trajectory (with box info)
NO ACTIONS WERE SPECIFIED
Processing AMBER trajectory file ../REMD-001.mdcrd
Set 1 .
WARNING in readAmberTrajectory(): Set #2 is corrupted (REMD 1 4 )...
PTRAJ: Successfully read in 1 sets and processed 1 sets.
       Dumping accumulated results (if any)

Regards,

Dr. Morad Mustafa

On Wednesday 12 August 2009 7:52:56 pm Carlos Simmerling wrote:
> what ptraj version? also please provide everything in the ptraj output
> up to the error msg.
>
> On 8/12/09, Morad Mustafa <alawneh_at_uga.edu> wrote:
> > Hi,
> >
> > I have carried out REMD using hybrid solvent model based on the tutorial
> > from the web and the
> > archive notes. In my simulation, I use Amber 10.
> > I have an issue with reading the REMD trajectories. The ptraj reads only
> > one frame out of 500
> > frames.
> > How can I analyze those types of REMD trajectories if ptraj does not read
> > them?
> >
> > This is the script I used for reading the REMD trajectories:
> > #!/bin/csh
> >
> > set Replica_First = 1
> > set Replica_Last = 1
> > set PrmTop = "../../Modeling/EGFR-WT_active.prmtop"
> > set Process = "REMD"
> >
> > set Replica = $Replica_First
> >
> > while ($Replica <= $Replica_Last)
> > set RepID = `printf "%3.3i" $Replica`
> > set TrajIn = "../${Process}-${RepID}.mdcrd"
> > set TrajOut = "${Process}-${RepID}-Test.mdcrd"
> > ptraj $PrmTop << EOF
> > trajin $TrajIn remdtraj
> > trajout $TrajOut
> > EOF
> > @ Replica = ($Replica + 1)
> > end
> >
> > Here is part of the outputs:
> > PTRAJ: Processing input from "STDIN" ...
> >
> > PTRAJ: trajin ../REMD-001.mdcrd remdtraj
> > Checking coordinates: ../REMD-001.mdcrd
> >
> > PTRAJ: trajout REMD-001-Test.mdcrd
> >
> > PTRAJ: Successfully read the input file.
> > Coordinate processing will occur on 500 frames.
> > Summary of I/O and actions follows:
> >
> > INPUT COORDINATE FILES
> > File (../REMD-001.mdcrd) is an AMBER trajectory (with box info) with
> > 500 sets
> >
> > OUTPUT COORDINATE FILE
> > File (REMD-001-Test.mdcrd) is an AMBER trajectory (with box info)
> >
> > NO ACTIONS WERE SPECIFIED
> >
> > Processing AMBER trajectory file ../REMD-001.mdcrd
> >
> > Set 1 .
> > WARNING in readAmberTrajectory(): Set #2 is corrupted (REMD 1
> > 4 )...
> >
> >
> >
> > PTRAJ: Successfully read in 1 sets and processed 1 sets.
> > Dumping accumulated results (if any)
> >
> >
> > This is the REMD.in
> > Replica Exchange Molecular Dynamics Run
> > &cntrl
> > ! Minimization Flags
> > imin = 0,
> > maxcyc = 1,
> > ncyc = 500,
> > ntmin = 1,
> > ! Input Format
> > ntx = 1,
> > irest = 0,
> > ! Output Format and Frequency
> > ntpr = 500,
> > ntave = 0,
> > ntwr = 5000,
> > iwrap = 1,
> > ntwx = 1000,
> > ntwv = 0,
> > ntwe = 0,
> > ntwprt = 0,
> > idecomp = 0,
> > ! Harmonically Restrained Atoms
> > ntr = 0,
> > !restraint_wt = ,
> > !restraintmask= ,
> > ! MD Parameters
> > nstlim = 500,
> > numexchg= 1000,
> > nscm = 500,
> > t = 0.0,
> > dt = 0.002,
> > nrespa = 2,
> > ! Temperature Regulation
> > ntt = 3,
> > temp0 = 298.15,
> > tempi = 298.15,
> > ig = 12993,
> > tautp = 1.0,
> > gamma_ln= 1.0,
> > ! Pressure Regulation
> > ntp = 0,
> > pres0 = 1.0,
> > taup = 2.0,
> > ! SHAKE Parameters
> > ntc = 2,
> > ! Potential Function Parameters
> > ntf = 2,
> > ntb = 1,
> > cut = 12.0,
> > scnb = 2.0,
> > scee = 1.2,
> > nsnb = 25,
> > igb = 0,
> > hybridgb= 5,
> > numwatkeep = 1000,
> > ipol = 0,
> > ifqnt = 0,
> > /
> > &ewald
> > nfft1 = 128,
> > nfft2 = 128,
> > nfft3 = 128,
> > order = 6,
> > verbose = 0,
> > ew_type = 0,
> > nbflag = 1,
> > skinnb = 2.0,
> > netfrc = 1,
> > vdwmeth = 1,
> > column_fft = 1,
> > /
> >
> >
> > This is how the topology file was prepared:
> > # Load a force field
> > source "/usr/local/amber10/dat/leap/cmd/leaprc.ff03.r1"
> >
> > # Use implicit solvent model
> > set default PBradii bondi
> >
> > # Load in a pdb file.
> > Seq_List = {
> > NGLY GLU ALA PRO ASN GLN ALA LEU LEU ARG ILE LEU LYS
> > GLU THR GLU PHE LYS LYS ILE LYS VAL LEU GLY SER GLY
> > ALA PHE GLY THR VAL TYR LYS GLY LEU TRP ILE PRO GLU
> > GLY GLU LYS VAL LYS ILE PRO VAL ALA ILE LYS GLU LEU
> > ARG GLU ALA THR SER PRO LYS ALA ASN LYS GLU ILE LEU
> > ASP GLU ALA TYR VAL MET ALA SER VAL ASP ASN PRO HIS
> > VAL CYS ARG LEU LEU GLY ILE CYS LEU THR SER THR VAL
> > GLN LEU ILE THR GLN LEU MET PRO PHE GLY CYS LEU LEU
> > ASP TYR VAL ARG GLU HIS LYS ASP ASN ILE GLY SER GLN
> > TYR LEU LEU ASN TRP CYS VAL GLN ILE ALA LYS GLY MET
> > ASN TYR LEU GLU ASP ARG ARG LEU VAL HIS ARG ASP LEU
> > ALA ALA ARG ASN VAL LEU VAL LYS THR PRO GLN HIS VAL
> > LYS ILE THR ASP PHE GLY LEU ALA LYS LEU LEU GLY ALA
> > GLU GLU LYS GLU TYR HIS ALA GLU GLY GLY LYS VAL PRO
> > ILE LYS TRP MET ALA LEU GLU SER ILE LEU HIS ARG ILE
> > TYR THR HIS GLN SER ASP VAL TRP SER TYR GLY VAL THR
> > VAL TRP GLU LEU MET THR PHE GLY SER LYS PRO TYR ASP
> > GLY ILE PRO ALA SER GLU ILE SER SER ILE LEU GLU LYS
> > GLY GLU ARG LEU PRO GLN PRO PRO ILE CYS THR ILE ASP
> > VAL TYR MET ILE MET VAL LYS CYS TRP MET ILE ASP ALA
> > ASP SER ARG PRO LYS PHE ARG GLU LEU ILE ILE GLU PHE
> > SER LYS MET ALA ARG ASP PRO GLN ARG TYR LEU VAL ILE
> > GLN GLY ASP GLU ARG MET HIS LEU PRO SER PRO THR ASP
> > SER ASN PHE TYR ARG ALA LEU MET ASP GLU GLU ASP MET
> > ASP ASP VAL VAL ASP ALA ASP GLU TYR LEU CILE }
> > # PRO CGLN }
> > # GLN GLY }
> >
> > Protein = loadPdbUsingSeq "EGFR-WT_active_equil.pdb" Seq_List
> >
> > # Neutralize the protein
> > addIons Protein K+ 0
> >
> > # Solvate the protein with the right water model
> > solvateBox Protein TIP3PBOX 5.0
> >
> > # Save the prmtop and inpcrd files
> > saveAmberParm Protein "EGFR-WT_active.prmtop" "EGFR-WT_active.mdcrd"
> > savePdb Protein "EGFR-WT_active.pdb"
> >
> > quit
> >
> >
> > Regards,
> >
> > Dr. Morad Mustafa
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber

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