AMBER Archive (2006)

Subject: AMBER: MMPBSA & PBCAL

From: Rabal Gracia Marķa Obdulia (mariarabalg_at_iqs.es)
Date: Fri Mar 31 2006 - 09:37:57 CST

Dear Amber Users,
 
I am running MM-PBSA calculations with the PB term calculated by DELPHI (Amber8).

When calculating the corrected reaction-field energy of the ligand, it returns a null value.
>From the output in DELPHI, it seems that it properly reads the file.crg and file.siz and it assigns the corresponding values to the coordinates.
 
The files of the charges and the radii were extracted from one snapshot of the corresponding complex by using ptraj and the PARSE option in AMBER8, so they also include the protein parameters:

> trajin snap_com.crd.1
> trajout complejo.pdb pdb parse nowrap
 
I attach the correponding file.siz, file.crg, the input and output from Delphi and
the corresponding pdb linked to fort.13 unit (as extracted by ambpdb in <<cargas.crg>> <<delphi.prm.0.0>> <<radios.siz>> <<snap_lig.delphilog.1.0.0>> <<snap_lig.pdb.1>> mm_pbsa_calceneent.pm).
 
Any help or commentary will be appretiated!






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