AMBER Archive (2009)

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

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Aug 13 2009 - 11:25:32 CDT

Hi Tom,
I have a feeling that we might have a version problem. Your output
starts with 4/04/2008, and mine has 2/15/2008. Not sure if the year is
correct, but there is a date discrepancy. I downloaded the latest
AmberTools a couple of weeks ago, but that version gives me an endless
list of parsing errors. I quoted a part of the output below the message.
It looks like the ptraj fixes that were mentioned earlier this year
didn't make it to the official distribution for some reason.

Is there a way I could get the updated source code for ptraj? I've
downloaded the distro from ambermd three times in the past two weeks,
patched the bugfix and compiled it, but with the same result. So it's
pretty certain that it doesn't have your version of ptraj...

Thanks, Tom

Sasha

Output of my version of ptraj follows:

  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
  -/- Executable is: "/data/amber10/exe/ptraj"
  /-\
  \-/ Error scanning a value: parm->NBONH
Error scanning a value: parm->NBONA
Error scanning a value: parm->NTHETH
Error scanning a value: parm->NTHETA
Error scanning a value: parm->NPHIH
Error scanning a value: parm->NPHIA
Error scanning a value: parm->JHPARM
Error scanning a value: parm->JPARM
Error scanning a value: parm->NEXT
Error scanning a value: parm->NTOTRS
Error scanning a value: parm->MBONA
Error scanning a value: parm->MTHETS
Error scanning a value: parm->MPHIA
Error scanning a value: parm->MUMBND
Error scanning a value: parm->MUMANG
Error scanning a value: parm->MPTRA
Error scanning a value: parm->NATYP
Error scanning a value: parm->NHB
Error scanning a value: parm->IFPERT
Error scanning a value: parm->NBPER
Error scanning a value: parm->NGPER
Error scanning a value: parm->NDPER
Error scanning a value: parm->MBPER
Error scanning a value: parm->MGPER
Error scanning a value: parm->MDPER
Error scanning a value: parm->IFBOX
Error scanning a value: parm->NMXRS
Error scanning a value: parm->IFCAP

WARNING in scanDouble: ...scanning chrg

WARNING in scanDouble: ...scanning chrg

WARNING in scanDouble: ...scanning chrg

WARNING in scanDouble: ...scanning chrg

......more of the same....

WARNING in scanDouble: ...scanning pert, cgper

Error scanning a value: LES, nlestyp
Error scanning a value: LES, lestyp
Error scanning a value: LES, lestyp
Error scanning a value: LES, lestyp
Error scanning a value: LES, lestyp
Error scanning a value: LES, lestyp
Error scanning a value: LES, lescnum
Error scanning a value: LES, lescnum
Error scanning a value: LES, lescnum
Error scanning a value: LES, lescnum
Error scanning a value: LES, lessubsp
Error scanning a value: LES, lessubsp
Error scanning a value: LES, lessubsp
Error scanning a value: LES, lessubsp

Thomas Cheatham wrote:
>> 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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