AMBER Archive (2004)

Subject: AMBER: about running ptraj in ambber8 (re-post)

From: jz7_at_duke.edu
Date: Mon Jul 26 2004 - 15:47:52 CDT

Dear all,

I was trying to run ptraj in Amber8. But it has problem to read Charmm
format file (topology psf file). I am wondering if there is any defaut
Amber format setting?

I tried it on the old independent ptraj version (not imbedded in Amber,
and I downloaded from Dr. Thomas Cheatham's website), it worked.
Any idea why this happened?

Thanks a lot!

PS: there are 2 parts in the following text. Part 1 is my psf file; part 2
is the error message in ptraj.

The following is my psf file. It's very long, so I'll just paste the beginning:

 PSF

        1 !NTITLE
  REMARKS original generated structure x-plor psf file

    60787 !NATOM
        1 PRO1 1 ALA N NH3 -0.300000 14.0070 0
        2 PRO1 1 ALA HT1 HC 0.330000 1.0080 0
        3 PRO1 1 ALA HT2 HC 0.330000 1.0080 0
        4 PRO1 1 ALA HT3 HC 0.330000 1.0080 0
        5 PRO1 1 ALA CA CT1 0.210000 12.0110 0
        6 PRO1 1 ALA HA HB 0.100000 1.0080 0
        7 PRO1 1 ALA CB CT3 -0.270000 12.0110 0
        8 PRO1 1 ALA HB1 HA 0.090000 1.0080 0
        9 PRO1 1 ALA HB2 HA 0.090000 1.0080 0
       10 PRO1 1 ALA HB3 HA 0.090000 1.0080 0
       11 PRO1 1 ALA C C 0.510000 12.0110 0
       12 PRO1 1 ALA O O -0.510000 15.9990 0
       13 PRO1 2 GLU N NH1 -0.470000 14.0070 0
       14 PRO1 2 GLU HN H 0.310000 1.0080 0
       15 PRO1 2 GLU CA CT1 0.070000 12.0110 0
       16 PRO1 2 GLU HA HB 0.090000 1.0080 0
       17 PRO1 2 GLU CB CT2 -0.180000 12.0110 0
       18 PRO1 2 GLU HB1 HA 0.090000 1.0080 0

And the error message in ptraj is the following:

Input the name of an AMBER prmtop or CHARMM PSF: test-ionized.psf
Opened file test-ionized.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->MDPER
Error scanning a value: parm->IFBOX
Error scanning a value: parm->NMXRS
Error scanning a value: parm->IFCAP
Read in control variables
Read in atom names...
Read in charges...

ERROR in scanDouble: ...scanning amass

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

Read in the residue to atom pointer list...
ERROR in scanDouble: ...scanning req

Read in bond parameters RK and REQ...

ERROR in scanDouble: ...scanning tk

ERROR in scanDouble: ...scanning teq

Read in angle parameters TK and TEQ...

ERROR in scanDouble: ...scanning pk

ERROR in scanDouble: ...scanning pn

ERROR in scanDouble: ...scanning phase

Read in dihedral parameters PK, PN and PHASE...

ERROR in scanDouble: ...scanning solty

Read in SOLTY...

ERROR in scanDouble: ...scanning cn1

ERROR in scanDouble: ...scanning cn2

Read in L-J parameters CN1 and CN2...
Error scanning a value: bonds with hydrogen, IB
Error scanning a value: bonds with hydrogen, JB
Error scanning a value: bonds with hydrogen, ICB
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Error scanning a value: angles with hydrogen, ICT
Read in info for angles w/ hydrogen...
Error scanning a value: angles without hydrogen, ICT
Read in info for angles w/out hydrogen...
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, ICP
Read in info for dihedrals w/ hydrogen...
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, ICP
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...

ERROR in scanDouble: ...scanning bg

ERROR in scanDouble: ...scanning hbcut

Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...

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