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. the command is:
" 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 hint 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,
Duan Baogen
Beijing Computational Science Research Center
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Received on Tue Oct 02 2012 - 20:30:04 PDT
