Dear All,
I am a pretty new user of Amber package so please respond to this e-mail if
you have any clue to my problem with using Amber . I ran the md
simulations for the wild-type and one of the mutants of human carbonic
anhydrase protrein with NAMD, I have generated the Charmm psf files and the
dcd trajectory files for both the systems. Now I'd like to analyse my
trajectory by using the ptraj utility of Amber package. We have the Amber
installed (amber 9) with x86_64 GNU/LINUX machine in our lab. Firstly, I
tried running the in-built ptraj utility of that package. Then this showed
couple of warning messages with reading the parameter files followed by a
segmentation fault. Next I searched though your mailing list and found that
there might be some problem with running the ptraj with Charmm psf file in
the older version of Amber. Then I installed the Ambertool 1.2 to check
whether the above problem got fixed by using that or not. But still its
showing couple of error messages like the following:
Error scanning a value: angles without hydrogen, JT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, ICT
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, IP
WARNING in scanDouble: ...scanning ag
WARNING in scanDouble: ...scanning bg
WARNING in scanDouble: ...scanning hbcut
Warning: Scanned \n for character 3; replacing with space
Error scanning a value: join info
Error scanning a value: irotat info
Error scanning a value: box information, nspsol
Error scanning a value: box information, nsp
WARNING in scanDouble: ...scanning box, box[1]
WARNING in scanDouble: ...scanning box, box[2]
Scanning Cap; this has not been debugged!
Error scanning a value: cap information, cap
WARNING in scanDouble: ...scanning cap, ycap
WARNING 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
Error scanning a value: pert, icbper
Angles...
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Dihedrals...
Error scanning a value: pert, kpper
Error scanning a value: pert, lpper
Error scanning a value: pert, ipper
Error scanning a value: pert, jpper
Extra perturbation information...
Warning: Scanned \n for character 3; replacing with space
Warning: Scanned \n for character 3; replacing with space
Warning: Scanned \n for character 3; replacing with space
WARNING in scanDouble: ...scanning pert, almper
Error scanning a value: pert, iaper
Error scanning a value: pert, iacper
WARNING in scanDouble: ...scanning pert, cgper
There were errors upon reading parm file!!!
RDPARM MENU. Please enter commands. Use "?" or "help"
for more info. "exit" or "quit" to leave program...
Then after giving the command:
ptraj H107Y_all.psf < ptraj.in it proceeds and give me the following
feedback:
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin H107Y_eq1_new_300.dcd.bz2 1 500 1
Checking coordinates: H107Y_eq1_new_300.dcd.bz2
WARNING in checkCoordinates(): The actual number of atoms (46844)
does not match the expected number of atoms (19) in
(H107Y_eq1_new_300.dcd.bz2)
With this version of the code, this will likely lead to program failure!!!
PTRAJ: rms first out rmsd.dat
Mask [*] represents 19 atoms
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 500 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (H107Y_eq1_new_300.dcd.bz2) is a CHARMM trajectory in big endian
binary format
with box information representing 500 sets
NFILE = 2706 ISTEP = 300250 NINTV = 250 NSAVC = 976500 NSAVV
= 0
NDEGF = 0 NFREA = 0 DELTA = 0.0409 QCRYS = 1 QDIM4
= 0
VERNU = 24 NATREC= 46844 NFREAT = 46844
Dumping the title:
REMARKS FILENAME=H107Y_eq1_new_300.dcd CREATED BY
NAMD
REMARKS DATE: 08/02/11 CREATED BY USER:
puspita
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> RMS to first frame using no mass weighting
Dumping RMSd vs. time (with time interval 1.00) to a file named
rmsd.dat
Atom selection follows * (All atoms are selected)
Processing CHARMM trajectory file H107Y_eq1_new_300.dcd.bz2
Segmentation fault
My ptraj.in file looks like this
ptraj H107Y_all.psf << EOF
trajin H107Y_eq1_new_300.dcd.bz2 1 500 1
rms first out rmsd.dat
EOF
It talks about atom numbers mismatch between the psf and the dcd file which
is not understandable to me. Is there any atom number limitations for
running ptraj? I used the same psf and dcd files for some of the analysis
in namd (like rmsd calculations and so on) and it went well. If you want me
to send the psf and dcd files I can send that too.
Thanks for your help in advance.
Puspita
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Received on Thu Nov 24 2011 - 22:30:04 PST
