Hi AMBER lovers,
I am a newer in using AMBER. Now I met some problem when I am using AMBER, and
wish to hear from your suggestion and advices. Thank you so much in advance!
I am using AMBER 7 to conduct MD simulations on a system containing a tetramer
protein (4*428 residues)with cofactor NAD+, and water molecules. I have used
ptraj and carnal to do some analysis, and the trajectories are OK to be
analyzed.
Now I want to convert the trajectories generated by AMBER to CHARMM format to
some other analysis. Following is my ptraj input file for conversion:
trajin 1b3r_sol_eq1.crd
trajin 1b3r_sol_eq2.crd
trajin 1b3r_sol_eq3.crd
trajin 1b3r_sol_md1.crd
trajin 1b3r_sol_md2.crd
center :1-1732
image center familiar
strip :WAT
strip :Na+
trajout 1b3r_5ns_charmm.cor nobox charmm little
However, it seems that the converted trajectory is not OK to be used in
CHARMM31. Following is the error information in CHARMM output file:
READING TRAJECTORY FROM UNIT 21
NUMBER OF COORDINATE SETS IN FILE: 0
NUMBER OF PREVIOUS DYNAMICS STEPS: 0
FREQUENCY FOR SAVING COORDINATES: 0
NUMBER OF STEPS FOR CREATION RUN: 0
***** ERROR ***** NO. OF ATOMS DO NOT MATCH 26796********
*** LEVEL -4 WARNING *** BOMLEV IS -1
BOMLEV HAS BEEN SATISFIED. TERMINATING.
I am so puzzled that why CHARMM can't read any frame from the converted
trajectory.
I noticed that the atom names are differnet in two format. I compared the psf
file I generated in CHARMM (no water) and the pdb file extracted from AMBER
trajectory (no water). The total atom numbers are same. The atoms in protein
are same in sequence, but differnet in atom name. The atoms in NAD are
different either in sequence or atom name. But I am wondering that if this is
the problem, CHARMM should be able to read some frame from the trajectory and
complain the inconsistence on atom names.
Thank you so much again for your time and suggestion.
Best wishes
Yours
Chen Hu
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Received on Sat Apr 23 2005 - 23:53:00 PDT
