AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Aug 12 2009 - 18:54:20 CDT

what ptraj version? also, include the entire 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
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
Stony Brook University           E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================

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