Dear Amber users and developers,
I want to use the MM-PBSA script to analyze the binding energy between
protein and small ligand. Firstly, charmm force field is used to carry out
MD simulation using NAMD software. Secondly, the DCD file is converted to
crd file using catdcd. Meanwhile, psf and pdb file in Charmm format should
be converted to corresponding amber crd and top files. This can be
completed by chamber program in Amber sofrware. the command used is as
follow
" chamber -top top_all27_prot_na_mod.inp -param par_all27_prot_na.prm -psf
atp.psf -crd atp.pdb -nocmap "
But error occurrs. the error message is "At line 2178 of file _psfprm.f
Fortran runtime error: End of file". Would you like to give me some help?
Thank you in advance! The corresponding files are enclosed.
Best wishes,
Yours sincerely
Duan Baogen
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Received on Thu Oct 11 2012 - 19:30:02 PDT
