AMBER Archive (2009)

Subject: [AMBER] Protein with HETATM, am I doing the right thing

From: nicholus bhattacharjee (
Date: Thu May 21 2009 - 06:21:15 CDT

Dear all,
             My protein contains HETATM PO4. Since these residues are not
recognized by in leap I used antechber in the following way.

1. Made a file of HETATM po4 (filename).
3. tleap
4. source leaprc.gaff
5. source leaprc.ff99SB
6. antechamber -i po4 -fi pdb -o po4.prepin -fo prepi -c bcc -s 2 -c -3
7. parmchk -i po4.prepin -f prepi -o po4.frcmod
8. mol=loadpdb pdb(main pdb file)

Please can anyone suggest me am I doing the right thing because with running
antechber on po4 dose not generate divcon files but the after that the
parameter files can be generated. I shall be great full for the suggestion.

Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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