AMBER Archive (2009)

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

From: Amit Bajaj (amit_at_dmsystems.in)
Date: Thu May 21 2009 - 00:26:49 CDT

dear nicholus,

may we know under whom you are pursuing Phd, we are based out of delhi, may be we can help

Thanks

Best rgds

Amit

D M Systems Pvt. Ltd.

B-127, Shivalik, ND – 17

Ph – 26691429/2344

98112-07764

“ One never reaches anywhere sitting on the shore”

----- Original Message -----
From: "nicholus bhattacharjee" <nicholusbhattacharjee_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Thursday, May 21, 2009 10:18:42 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: [AMBER] Protein with HETATM, am I doing the

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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