AMBER Archive (2004)

Subject: AMBER: about running ptraj in amber8

From: jz7_at_duke.edu
Date: Mon Jul 26 2004 - 09:04:33 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 ptraj version (seperated from
Amber), it worked. Any idea why this happened?

Thanks a lot!

The following is the error message:

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...
Error scanning a value: join info
Read in the JOIN info...
Read in the IROTAT info...
Scanning Box
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp

ERROR in scanDouble: ...scanning box, box[0]

ERROR in scanDouble: ...scanning box, box[1]

ERROR in scanDouble: ...scanning box, box[2]

Read in box information...
Scanning Cap; this has not been debugged!
Error scanning a value: cap information, cap

ERROR in scanDouble: ...scanning cap, xcap

ERROR in scanDouble: ...scanning cap, ycap

ERROR in scanDouble: ...scanning cap, zcap

WARNING: an error upon reading the parm file has
been reported. Proceed with caution since some of
the data for the current parm file may be undefined
Scanning Perturbation info...
  Bonds...
Error scanning a value: pert, ibper
Error scanning a value: pert, jbper
  Angles...
  Dihedrals...
Error scanning a value: pert, lpper
  Extra perturbation information...
Reading in LES information...
Error scanning a value: LES, nlestyp
Error scanning a value: LES, lescnum
There were errors upon reading parm file!!!

Initializing state: detected PBC beta angle in prmtop that is not 90.0!

PTRAJ: Processing input file...
       Input is from standard input

On Fri, 23 Jul 2004, Michael Peterson wrote:

> On Fri, 2004-07-23 at 17:43, jz7_at_duke.edu wrote:
> > How should I use the ptraj under Amber8? The automatic path of ptraj goes
> > to amber7.
> >
> > Thanks!
>
> instead of the "set path.." line below, do this instead:
> set path=( $AMBERHOME $path )
> rehash
>
> Also, don't use igor4 -- it doesn't have the necessary libraries. Use
> either igor2 or yogi14, your workstation.
>
> Michael
>
>
> > On Fri, 23 Jul 2004, Michael Peterson wrote:
> >
> > > On Fri, 2004-07-23 at 15:29, jz7_at_duke.edu wrote:
> > > > Hi Michael,
> > > >
> > > > Any luck on the installation of Amber8?
> > > >
> > > > Thanks a lot!
> > > >
> > > > Jieru
> > >
> > > I haven't quite finished the complete testing and installation, but you
> > > can give it a try on igor2 and igor4. Once you login, give the
> > > following commands:
> > > setenv AMBERHOME /xtmp/map/amber8
> > > set path=( $path $AMBERHOME/exe )
> > > and you should start to use the new AMBER 8. If you have set AMBERHOME
> > > in your .cshrc file or added $AMBERHOME/exe to your path in your .cshrc
> > > file, comment those out before logging into igor2 or igor4.
> > >
> > > Please let me know how they work for you.
> > > Michael
> > > --
> > > Michael A. Peterson, PhD.
> > > Computational Chemistry Systems Administrator
> > > Department of Chemistry
> > > Duke University
> > > 919.660.1646
> > >
> > >
> --
> Michael A. Peterson, PhD.
> Computational Chemistry Systems Administrator
> Department of Chemistry
> Duke University
> 919.660.1646
>
>
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