AMBER Archive (2009)

Subject: Re: [AMBER] ptraj failure to parse psf input

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Aug 12 2009 - 23:27:34 CDT

> fails on larger systems (at least, in my observations). For instance,
> 27000 atom system is parsed correctly, but 75000+ fails. I'm attaching a
> compressed psf file that ptraj is unable to parse. I use 64-bit CentOS
> on a Xeon system.
> I would greatly appreciate any suggestions.

What is the failure? I just tried this with AMBER10 and my development
version of ptraj and did not see a failure. I need more information to
help out...

(however I do have concern that the box lengths came out to zero!)

--tom

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

~/AMBER/amber10/exe/ptraj blank_his3_autopsf.psf

  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AmberTools 1.0.1 integrated" (4/04/2008)
  -/- Executable is: "/uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber10/exe/ptraj"
  /-\
  \-/ Reading in CHARMM PSF file
Reading in the title...

 REMARKS original generated structure x-plor psf file
 REMARKS 2 patches were applied to the molecule.
 REMARKS topology /usr/local/lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top
 REMARKS topology blank_his3_autopsf-temp.top
 REMARKS topology /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.2/wat.top
 REMARKS segment P1 { first NTER; last CTER; auto angles dihedrals }
 REMARKS segment WT1 { first NONE; last NONE; auto none }
 REMARKS segment WT2 { first NONE; last NONE; auto none }
 REMARKS segment WT3 { first NONE; last NONE; auto none }
 REMARKS segment WT4 { first NONE; last NONE; auto none }
 REMARKS segment WT5 { first NONE; last NONE; auto none }
 REMARKS segment WT6 { first NONE; last NONE; auto none }
 REMARKS segment WT7 { first NONE; last NONE; auto none }
 REMARKS segment WT8 { first NONE; last NONE; auto none }
 REMARKS segment ION { first NONE; last NONE; auto none }
 REMARKS patch NTER P1:1
 REMARKS patch CTER P1:419

Total number is atoms is 75276
Reading in the atom information...
Dumping out residue names:
 VAL ILE THR PHE PRO THR ASN VAL ALA THR
 MET PRO GLU PHE ARG SER TRP ALA ARG GLY
 LYS LEU ASP ILE ASP GLN ASP SER ILE GLY
 TRP TYR PHE LYS TYR LEU ASP PRO ALA GLY
 ALA THR GLU SER ALA ARG ALA VAL GLY GLU
 TYR SER LYS ILE PRO ASP GLY LEU VAL LYS
 PHE SER VAL ASP ALA GLU ILE ARG GLU ILE
 TYR ASN GLU GLU CYS PRO THR VAL SER ASP
 ALA SER ILE PRO LEU ASP GLY ALA GLN TRP
 SER LEU SER ILE ILE SER TYR PRO MET PHE
 ARG THR ALA TYR PHE ALA VAL ALA ASN VAL
 ASP ASN LYS GLU ILE SER LEU ASP VAL THR
 ASN ASP LEU ILE VAL TRP LEU ASN ASN LEU
 ALA SER TRP ARG ASP VAL VAL ASP SER GLY
 GLN TRP PHE THR PHE ALA GLY SER HSD HSD
 HSD HSD HSD HSD GLY ALA SER ASP ASP PRO
 THR TRP PHE VAL ARG ILE ARG VAL LEU HSD
 PRO THR TYR ASP LEU PRO ASP PRO THR GLU
 GLY LEU LEU ARG THR VAL SER ASP TYR ARG
 LEU THR TYR LYS SER ILE THR CYS GLU ALA
 ASN MET PRO THR LEU VAL ASP GLN GLY PHE
 TRP ILE GLY GLY HSD TYR ALA LEU THR PRO
 ILE ALA THR THR GLN ASN ALA VAL GLU GLY
 SER SER SER GLY GLY THR ALA ALA SER ASN
 ARG SER GLU VAL PRO LEU PRO PRO LEU THR
 PHE GLY GLN THR ALA PRO ASN ASN PRO LYS
 ILE GLU GLN THR LEU VAL LYS ASP THR LEU
 GLY SER TYR LEU VAL HSD SER LYS MET ARG
 ASN PRO VAL PHE GLN LEU THR PRO ALA SER
 SER PHE GLY ALA ILE SER PHE THR ASN PRO
 GLY PHE ASP ARG ASN LEU ASP LEU PRO GLY
 PHE GLY GLY ILE ARG ASP SER LEU ASP VAL
 ASN MET SER THR ALA VAL CYS HSD PHE ARG
 SER LEU SER LYS SER CYS SER ILE VAL THR
 LYS THR TYR GLN GLY TRP GLU GLY VAL THR
 ASN VAL ASN THR PRO PHE GLY GLN PHE ALA
 HSD SER GLY LEU LEU LYS ASN ASP GLU ILE
 LEU CYS LEU ALA ASP ASP LEU ALA THR ARG
 LEU THR GLY VAL TYR GLY ALA THR ASP ASN
 PHE ALA ALA ALA VAL LEU ALA PHE ALA ALA
 ASN MET LEU THR SER VAL LEU LYS SER GLU
 ALA THR THR SER VAL ILE LYS GLU LEU TIP3
 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3
 ...
 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 SOD SOD
 SOD SOD SOD SOD SOD SOD SOD SOD SOD SOD
 ...
 SOD SOD SOD SOD CLA CLA CLA CLA CLA CLA
 CLA CLA CLA CLA CLA CLA CLA CLA CLA CLA
 ...
 CLA CLA CLA CLA CLA
Dumping state information...
  atoms: 75276
  residues: 23535
  box length: 0.000 0.000 0.000
  box angles: 90.000 90.000 90.000
  molecules: 10
  max frames: 0
  solvent molecules: 22899 (68697 atoms)
  solvent mask is: :420-23318

PTRAJ: Processing input from "STDIN" ...

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