AMBER Archive (2006)

Subject: AMBER: reading psf file

From: jojartb_at_pharm.u-szeged.hu
Date: Fri Nov 17 2006 - 17:24:24 CST

Dear AMBER users,

i would like to analyze my namd job with amber ptraj.
is able ptraj to read in the psf file?
becuase i obtained the following erros:

Amber8 Module: ptraj

Input the name of an AMBER prmtop or CHARMM PSF: 128_dspc_wat.psf
Opened file 128_dspc_wat.psf with mode (r)
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->NMXRS
Error scanning a value: parm->IFCAP
Read in control variables
Read in atom names...

ERROR in scanDouble: ...scanning chrg

ERROR in scanDouble: ...scanning chrg

ERROR in scanDouble: ...scanning chrg

ERROR in scanDouble: ...scanning chrg

Read in charges...

ERROR in scanDouble: ...scanning amass

ERROR in scanDouble: ...scanning amass

ERROR in scanDouble: ...scanning amass

ERROR in scanDouble: ...scanning amass

Read in masses...
Error scanning a value: iac
Error scanning a value: iac
Error scanning a value: iac
Error scanning a value: iac
Read in IAC (atoms involved in L-J)...
Error scanning a value: numex
Error scanning a value: numex
Error scanning a value: numex
Read in NUMEX (index to excl atom list)...
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Error scanning a value: nno
Read in NNO (index for nonbond of @type)...
Read in residue labels...
         2 O1 1
Error scanning a value: ipres
Error scanning a value: ipres
Error scanning a value: ipres
segmantation fault.

with an another psf file (from vmd, alanin.psf):

Amber8 Module: ptraj

Input the name of an AMBER prmtop or CHARMM PSF: alanin.psf
Opened file alanin.psf with mode (r)
Reading in CHARMM PSF file
Reading in the title...

 REMARKS FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PSF"
 REMARKS PARAM11.PRO ( from PARAM6A )
 REMARKS ===========
 REMARKS PROTEIN PARAMETERS:
 REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4
 REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.
 REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 REMARKS
 REMARKS DATE:16-Feb-89 11:21:29 created by user: nonella

Total number is atoms is 66
Reading in the atom information...

ERROR in loadCharmmPSF(): Scanning atom information.

how can is solve this problem?

thank you for your helps in advance.

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