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Seems acpype has problems with unicode locales #4

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
alexxy@xeon /misc/_Work/acpypi $ ./acpype.py -i benz.pdb 
================================================================================
===============
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2011-03-01 15:03:57Z Rev: 364 
(c) 2011 AWSdS |
================================================================================
===============
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
ACPYPE FAILED: 'ascii' codec can't decode byte 0xd0 in position 1269: ordinal 
not in range(128)
Total time of execution: 1s
alexxy@xeon /misc/_Work/acpypi $ LANG=C ./acpype.py -i benz.pdb 
================================================================================
===============
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2011-03-01 15:03:57Z Rev: 364 
(c) 2011 AWSdS |
================================================================================
===============
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
==> AC output file present... doing nothing
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-I: Adding /misc/_Work/soft/amber11/dat/leap/prep to search path.
-I: Adding /misc/_Work/soft/amber11/dat/leap/lib to search path.
-I: Adding /misc/_Work/soft/amber11/dat/leap/parm to search path.
-I: Adding /misc/_Work/soft/amber11/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /misc/_Work/soft/amber11/dat/leap/cmd/leaprc.ff99SB
----- Source of /misc/_Work/soft/amber11/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /misc/_Work/soft/amber11/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)
Loading parameters: /misc/_Work/soft/amber11/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /misc/_Work/soft/amber11/dat/leap/lib/all_nucleic94.lib
Loading: DA
/misc/_Work/soft/amber11/bin/tleap: line 17: 26733 Segmentation fault      
$AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib 
-I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[gtkleap]$ [gtkleap]$ source leaprc.ff99SB
logFile leap.log
#
# ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
# -----  this file is updated for PDB format 3
#
#       load atom type hybridizations
#
addAtomTypes {
        { "H"   "H" "sp3" }
        { "HO"  "H" "sp3" }
        { "HS"  "H" "sp3" }
        { "H1"  "H" "sp3" }
        { "H2"  "H" "sp3" }
        { "H3"  "H" "sp3" }
        { "H4"  "H" "sp3" }
        { "H5"  "H" "sp3" }
        { "HW"  "H" "sp3" }
        { "HC"  "H" "sp3" }
        { "HA"  "H" "sp3" }
        { "HP"  "H" "sp3" }
        { "OH"  "O" "sp3" }
        { "OS"  "O" "sp3" }
        { "O"   "O" "sp2" }
        { "O2"  "O" "sp2" }
        { "OW"  "O" "sp3" }
        { "CT"  "C" "sp3" }
        { "CH"  "C" "sp3" }
        { "C2"  "C" "sp3" }
        { "C3"  "C" "sp3" }
        { "C"   "C" "sp2" }
        { "C*"  "C" "sp2" }
        { "CA"  "C" "sp2" }
        { "CB"  "C" "sp2" }
        { "CC"  "C" "sp2" }
        { "CN"  "C" "sp2" }
        { "CM"  "C" "sp2" }
        { "CK"  "C" "sp2" }
        { "CQ"  "C" "sp2" }
        { "CD"  "C" "sp2" }
        { "CE"  "C" "sp2" }
        { "CF"  "C" "sp2" }
        { "CP"  "C" "sp2" }
        { "CI"  "C" "sp2" }
        { "CJ"  "C" "sp2" }
        { "CW"  "C" "sp2" }
        { "CV"  "C" "sp2" }
        { "CR"  "C" "sp2" }
        { "CA"  "C" "sp2" }
        { "CY"  "C" "sp2" }
        { "C0"  "C" "sp2" }
        { "MG"  "Mg" "sp3" }
        { "N"   "N" "sp2" }
        { "NA"  "N" "sp2" }
        { "N2"  "N" "sp2" }
        { "N*"  "N" "sp2" }
        { "NP"  "N" "sp2" }
        { "NQ"  "N" "sp2" }
        { "NB"  "N" "sp2" }
        { "NC"  "N" "sp2" }
        { "NT"  "N" "sp3" }
        { "N3"  "N" "sp3" }
        { "S"   "S" "sp3" }
        { "SH"  "S" "sp3" }
        { "P"   "P" "sp3" }
        { "LP"  ""  "sp3" }
        { "F"   "F" "sp3" }
        { "CL"  "Cl" "sp3" }
        { "BR"  "Br" "sp3" }
        { "I"   "I"  "sp3" }
        { "FE"  "Fe" "sp3" }
        { "EP"  ""  "sp3" }
# glycam
        { "OG"  "O" "sp3" }
        { "OL"  "O" "sp3" }
        { "AC"  "C" "sp3" }
        { "EC"  "C" "sp3" }
}
#
#       Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
#
#       Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
#       Load main chain and terminating 
#       amino acid libraries (i.e. ff94 libs)
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
#
#       Load water and ions
# 
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
#       Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
  { 0 "G" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
  { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
  { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
  { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
}
addPdbAtomMap {
  { "O5*" "O5'" }
  { "C5*" "C5'" }
  { "C4*" "C4'" }
  { "O4*" "O4'" }
  { "C3*" "C3'" }
  { "O3*" "O3'" }
  { "C2*" "C2'" }
  { "C1*" "C1'" }
  { "C5M" "C7"  }
  { "O2*" "O2'" }
  { "H1*" "H1'" }
  { "H2*1" "H2'1" }
  { "H2*2" "H2'2" }
  { "H2'"  "H2'1" }
  { "H2''" "H2'2" }
  { "H3*" "H3'" }
  { "H4*" "H4'" }
  { "H5*1" "H5'1" }
  { "H5*2" "H5'2" }
  { "H5'"  "H5'1" }
  { "H5''" "H5'2" }
  { "HO2'" "HO'2" }
  { "HO5'" "H5T" }
  { "HO3'" "H3T" }
  { "O1'" "O4'" }
  { "OA"  "O1P" }
  { "OB"  "O2P" }
  { "OP1" "O1P" }
  { "OP2" "O2P" }
}
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
[gtkleap]$ source leaprc.gaff
logFile 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
Info: ignoring unknown atom type: cz
Info: while reading BOND. Input: cz nh  487.8    1.3391       SOURCE4      32   
0.0045
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si c3  189.8    1.8928       SOURCE4      77   
0.0061
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si ca  191.1    1.8898       SOURCE4      11   
0.0028
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si ha  186.3    1.4887       SOURCE4       6   
0.0040
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si oh  267.6    1.6792       SOURCE4       6   
0.0035
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si os  287.7    1.6524       SOURCE4      22   
0.0057
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si c3 c3   74.610     114.340  SOURCE4         
  26    1.1613
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si c3 h1   51.040     110.900  SOURCE4         
  17    1.0270
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si c3 hc   50.960     111.210  SOURCE4         
 222    0.4865
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si ca ca   73.850     121.430  SOURCE4         
  19    0.4235
Info: ignoring unknown atom type: h
Info: while reading ANGL. Input: f  c  h     0.000     109.900  SOURCE2         
   1    0.0000
Info: ignoring unknown atom type: h
Info: while reading ANGL. Input: h  c  o     0.000     127.300  SOURCE2         
   1    0.0000
Info: ignoring unknown atom type: cz
Info: while reading ANGL. Input: nh cz nh   72.970     120.170  SOURCE4         
  26    0.3964
Info: ignoring unknown atom type: cz
Info: while reading ANGL. Input: c3 nh cz   63.010     125.510  SOURCE4         
  12    0.5177
Info: ignoring unknown atom type: cz
Info: while reading ANGL. Input: cz nh hn   48.790     121.240  SOURCE4         
  40    0.5682
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si oh ho   52.570     115.710  SOURCE4         
   5    0.1738
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si os c3   74.830     124.640  SOURCE4         
   9    0.2879
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si c3   34.810     109.820  SOURCE4         
  88    0.5569
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si ca   34.800     110.090  SOURCE4         
  26    0.7331
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si oh   38.160     107.440  SOURCE4         
   8    1.5150
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si os   38.140     108.750  SOURCE4         
  38    0.7301
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: ha Si ha   19.530     108.770  SOURCE4         
   5    0.5372
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: os Si os   42.630     108.350  SOURCE4         
  15    1.7995
Info: ignoring unknown atom type: cb
Info: while reading DIHE. Input: X  c1 cb X    2    0.000       180.000         
  2.000     
Info: ignoring unknown atom type: cb
Info: while reading DIHE. Input: X  n1 cb X    2    0.000       180.000         
  2.000     
[gtkleap]$ set default fastbld on
[gtkleap]$ #set default disulfide auto
[gtkleap]$ LIG = loadpdb benz.pdb
Warning: cannot find template for residue LIG in our library.
         I am going to construct the template by myself.
         OK. I have fixed bond order and added hydrogens.
         Now I am calling antechamber to assign atom type and partial charge.

Total number of electrons: 42; net charge: 0

Running: /misc/_Work/soft/amber11/bin/sqm -O -i sqm.in -o sqm.out

Error: sparm type does not exist!
calling "mdlize_mdb( )"
    calling "mdlize_resd_bymdb( )"

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'benz_AC.prmtop'
Total time of execution: 1s

Original issue reported on code.google.com by alexx...@gmail.com on 8 Mar 2011 at 11:08

GoogleCodeExporter commented 9 years ago 
Can't reproduce this.

Can you tell me what's your locales?

Original comment by alanwil...@gmail.com on 14 Sep 2011 at 1:03

GoogleCodeExporter commented 9 years ago

Original comment by alanwil...@gmail.com on 22 Jul 2013 at 12:44