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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Received on Mon Jul 26 2004 - 21:53:00 PDT
