AMBER Archive (2009)

Subject: [AMBER] xleap problem

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Sun Jan 25 2009 - 05:49:28 CST

Dear All,
I¢m trying to get the prmtop and inpcrd files for my n-alkanes simulations with using xleap. My leap.log file is in below. I want to do MD simulations for 100 n-dodecane  molecules. I used packmol in order to get my pdb file that includes 100 n-dodecane  molecules. Then I started the minimization, but the min. progress stopped and I got an empty min.out file. I thought that I couldn¢t get the prmtop and inpcrd files  succesfully. Could you please help me to solve this problem and get prmtop and inpcrd files succesfully with xleap ?
Thanks in advance.
 
 
 Log file: ./leap.log
> #
> # ----- leaprc for loading the general Amber Force field.
> #       This file is mostly for use with Antechamber
> #
> #   load atom type hybridizations
> #
> addAtomTypes {
>     { "h1"  "H" "sp3" }
>     { "h2"  "H" "sp3" }
>     { "h3"  "H" "sp3" }
>     { "h4"  "H" "sp3" }
>     { "h5"  "H" "sp3" }
>     { "ha"  "H" "sp3" }
>     { "hc"  "H" "sp3" }
>     { "hn"  "H" "sp3" }
>     { "ho"  "H" "sp3" }
>     { "hp"  "H" "sp3" }
>     { "hs"  "H" "sp3" }
>     { "hw"  "H" "sp3" }
>     { "hx"  "H" "sp3" }
>     { "o"  "O" "sp2" }
>     { "o2"  "O" "sp2" }
>     { "oh"  "O" "sp3" }
>     { "os"  "O" "sp3" }
>     { "ow"  "O" "sp3" }
>     { "c"  "C" "sp2" }
>     { "c1"  "C" "sp2" }
>     { "c2"  "C" "sp2" }
>     { "c3"  "C" "sp3" }
>     { "ca"  "C" "sp2" }
>     { "cc"  "C" "sp2" }
>     { "cd"  "C" "sp2" }
>     { "ce"  "C" "sp2" }
>     { "cf"  "C" "sp2" }
>     { "cg"  "C" "sp2" }
>     { "ch"  "C" "sp2" }
>     { "cp"  "C" "sp2" }
>     { "cq"  "C" "sp2" }
>     { "cu"  "C" "sp2" }
>     { "cv"  "C" "sp2" }
>     { "cx"  "C" "sp2" }
>     { "cy"  "C" "sp2" }
>     { "n"   "N" "sp2" }
>     { "n1"  "N" "sp2" }
>     { "n2"  "N" "sp2" }
>     { "n3"  "N" "sp3" }
>     { "n4"  "N" "sp3" }
>     { "na"  "N" "sp2" }
>     { "nb"  "N" "sp2" }
>     { "nc"  "N" "sp2" }
>     { "nd"  "N" "sp2" }
>     { "ne"  "N" "sp2" }
>     { "nf"  "N" "sp2" }
>     { "nh"  "N" "sp2" }
>     { "no"  "N" "sp2" }
>     { "s"   "S" "sp2" }
>     { "s2"   "S" "sp2" }
>     { "s3"   "S" "sp3" }
>     { "s4"   "S" "sp3" }
>     { "s6"   "S" "sp3" }
>     { "sh"   "S" "sp3" }
>     { "ss"   "S" "sp3" }
>     { "sx"   "S" "sp3" }
>     { "sy"   "S" "sp3" }
>     { "p2"   "P" "sp2" }
>     { "p3"   "P" "sp3" }
>     { "p4"   "P" "sp3" }
>     { "p5"   "P" "sp3" }
>     { "pb"   "P" "sp3" }
>     { "pd"   "P" "sp3" }
>     { "px"   "P" "sp3" }
>     { "py"   "P" "sp3" }
>     { "f"   "F" "sp3" }
>     { "cl"  "Cl" "sp3" }
>     { "br"  "Br" "sp3" }
>     { "i"   "I"  "sp3" }
> }
> #
> #   Load the general force field parameter set.
> #
> gaff = loadamberparams gaff.dat
Loading parameters: /home_palamut2/software/application/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
 
> HELP
Help is available on the following subjects:
 
_cmd_options_       _types_             add                 addAtomTypes
addIons             addIons2            addPath             addPdbAtomMap
addPdbResMap        alias               alignAxes           bond
bondByDistance      center              charge              check
clearPdbAtomMap     clearPdbResMap      clearVariables      combine
copy                createAtom          createParmset       createResidue
createUnit          crossLink           debugOff            debugOn
debugStatus         deleteBond          deleteOffLibEntry   deleteRestraint
desc                deSelect            displayPdbAtomMap   displayPdbResMap
edit                groupSelectedAtoms  help                impose
list                listOff             loadAmberParams     loadAmberPrep
loadMol2            loadOff             loadPdb             loadPdbUsingSeq
logFile             matchVariables      measureGeom         quit
remove              restrainAngle       restrainBond        restrainTorsion
saveAmberParm       saveAmberParmPert   saveAmberParmPol    saveAmberParmPolPert
saveAmberPrep       saveOff             saveOffParm         savePdb
scaleCharges        select              sequence            set
setBox              solvateBox          solvateCap          solvateDontClip
solvateOct          solvateShell        source              transform
translate           verbosity           zMatrix            
 
For a list of the current aliases, type "alias".
> DEC = loadMol2 c12.AA.mol2
Loading Mol2 file: ./c12.AA.mol2
Reading MOLECULE named DEC
> charge DEC
Total unperturbed charge:   0.000000
Total perturbed charge:     0.000000
> check DEC
Checking 'DEC'....
Checking parameters for unit 'DEC'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> desc DEC
UNIT name: DEC
Head atom: null
Tail atom: null
Contents:
R<DEC 1>
> n-dodecane = loadpdb n-dodecane.packmol100.pdb
Loading PDB file: ./n-dodecane.packmol100.pdb
Enter zPdbReadScan from call depth  0.
Exit  zPdbReadScan from call depth  0.
Matching PDB residue names to LEaP variables.
(Residue 0: DEC, Terminal/last, was not found in name map.)
(Residue 1: DEC, Terminal/last, was not found in name map.)
(Residue 2: DEC, Terminal/last, was not found in name map.)
(Residue 3: DEC, Terminal/last, was not found in name map.)
(Residue 4: DEC, Terminal/last, was not found in name map.)
(Residue 5: DEC, Terminal/last, was not found in name map.)
(Residue 6: DEC, Terminal/last, was not found in name map.)
(Residue 7: DEC, Terminal/last, was not found in name map.)
(Residue 8: DEC, Terminal/last, was not found in name map.)
(Residue 9: DEC, Terminal/last, was not found in name map.)
(Residue 10: DEC, Terminal/last, was not found in name map.)
(Residue 11: DEC, Terminal/last, was not found in name map.)
(Residue 12: DEC, Terminal/last, was not found in name map.)
(Residue 13: DEC, Terminal/last, was not found in name map.)
(Residue 14: DEC, Terminal/last, was not found in name map.)
(Residue 15: DEC, Terminal/last, was not found in name map.)
(Residue 16: DEC, Terminal/last, was not found in name map.)
(Residue 17: DEC, Terminal/last, was not found in name map.)
(Residue 18: DEC, Terminal/last, was not found in name map.)
(Residue 19: DEC, Terminal/last, was not found in name map.)
(Residue 20: DEC, Terminal/last, was not found in name map.)
(Residue 21: DEC, Terminal/last, was not found in name map.)
(Residue 22: DEC, Terminal/last, was not found in name map.)
(Residue 23: DEC, Terminal/last, was not found in name map.)
(Residue 24: DEC, Terminal/last, was not found in name map.)
(Residue 25: DEC, Terminal/last, was not found in name map.)
(Residue 26: DEC, Terminal/last, was not found in name map.)
(Residue 27: DEC, Terminal/last, was not found in name map.)
(Residue 28: DEC, Terminal/last, was not found in name map.)
(Residue 29: DEC, Terminal/last, was not found in name map.)
(Residue 30: DEC, Terminal/last, was not found in name map.)
(Residue 31: DEC, Terminal/last, was not found in name map.)
(Residue 32: DEC, Terminal/last, was not found in name map.)
(Residue 33: DEC, Terminal/last, was not found in name map.)
(Residue 34: DEC, Terminal/last, was not found in name map.)
(Residue 35: DEC, Terminal/last, was not found in name map.)
(Residue 36: DEC, Terminal/last, was not found in name map.)
(Residue 37: DEC, Terminal/last, was not found in name map.)
(Residue 38: DEC, Terminal/last, was not found in name map.)
(Residue 39: DEC, Terminal/last, was not found in name map.)
(Residue 40: DEC, Terminal/last, was not found in name map.)
(Residue 41: DEC, Terminal/last, was not found in name map.)
(Residue 42: DEC, Terminal/last, was not found in name map.)
(Residue 43: DEC, Terminal/last, was not found in name map.)
(Residue 44: DEC, Terminal/last, was not found in name map.)
(Residue 45: DEC, Terminal/last, was not found in name map.)
(Residue 46: DEC, Terminal/last, was not found in name map.)
(Residue 47: DEC, Terminal/last, was not found in name map.)
(Residue 48: DEC, Terminal/last, was not found in name map.)
(Residue 49: DEC, Terminal/last, was not found in name map.)
(Residue 50: DEC, Terminal/last, was not found in name map.)
(Residue 51: DEC, Terminal/last, was not found in name map.)
(Residue 52: DEC, Terminal/last, was not found in name map.)
(Residue 53: DEC, Terminal/last, was not found in name map.)
(Residue 54: DEC, Terminal/last, was not found in name map.)
(Residue 55: DEC, Terminal/last, was not found in name map.)
(Residue 56: DEC, Terminal/last, was not found in name map.)
(Residue 57: DEC, Terminal/last, was not found in name map.)
(Residue 58: DEC, Terminal/last, was not found in name map.)
(Residue 59: DEC, Terminal/last, was not found in name map.)
(Residue 60: DEC, Terminal/last, was not found in name map.)
(Residue 61: DEC, Terminal/last, was not found in name map.)
(Residue 62: DEC, Terminal/last, was not found in name map.)
(Residue 63: DEC, Terminal/last, was not found in name map.)
(Residue 64: DEC, Terminal/last, was not found in name map.)
(Residue 65: DEC, Terminal/last, was not found in name map.)
(Residue 66: DEC, Terminal/last, was not found in name map.)
(Residue 67: DEC, Terminal/last, was not found in name map.)
(Residue 68: DEC, Terminal/last, was not found in name map.)
(Residue 69: DEC, Terminal/last, was not found in name map.)
(Residue 70: DEC, Terminal/last, was not found in name map.)
(Residue 71: DEC, Terminal/last, was not found in name map.)
(Residue 72: DEC, Terminal/last, was not found in name map.)
(Residue 73: DEC, Terminal/last, was not found in name map.)
(Residue 74: DEC, Terminal/last, was not found in name map.)
(Residue 75: DEC, Terminal/last, was not found in name map.)
(Residue 76: DEC, Terminal/last, was not found in name map.)
(Residue 77: DEC, Terminal/last, was not found in name map.)
(Residue 78: DEC, Terminal/last, was not found in name map.)
(Residue 79: DEC, Terminal/last, was not found in name map.)
(Residue 80: DEC, Terminal/last, was not found in name map.)
(Residue 81: DEC, Terminal/last, was not found in name map.)
(Residue 82: DEC, Terminal/last, was not found in name map.)
(Residue 83: DEC, Terminal/last, was not found in name map.)
(Residue 84: DEC, Terminal/last, was not found in name map.)
(Residue 85: DEC, Terminal/last, was not found in name map.)
(Residue 86: DEC, Terminal/last, was not found in name map.)
(Residue 87: DEC, Terminal/last, was not found in name map.)
(Residue 88: DEC, Terminal/last, was not found in name map.)
(Residue 89: DEC, Terminal/last, was not found in name map.)
(Residue 90: DEC, Terminal/last, was not found in name map.)
(Residue 91: DEC, Terminal/last, was not found in name map.)
(Residue 92: DEC, Terminal/last, was not found in name map.)
(Residue 93: DEC, Terminal/last, was not found in name map.)
(Residue 94: DEC, Terminal/last, was not found in name map.)
(Residue 95: DEC, Terminal/last, was not found in name map.)
(Residue 96: DEC, Terminal/last, was not found in name map.)
(Residue 97: DEC, Terminal/last, was not found in name map.)
(Residue 98: DEC, Terminal/last, was not found in name map.)
(Residue 99: DEC, Terminal/last, was not found in name map.)
  total atoms in file: 3800
> saveAmberParm n-dodecane n-dodecane.prmtop n-dodecane.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:
 
      res   total affected
 
      DEC   100
  )
 (no restraints)
> savepdb n-dodecane n-dodecane.leap.pdb
Writing pdb file: n-dodecane.leap.pdb
> QUIT
      Quit


  • application/octet-stream attachment: min.in






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