> 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" ...
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 22:19:35 PDT
