AMBER Archive (2009)

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

From: amit (amit_at_dmsystems.in)
Date: Mon May 25 2009 - 10:26:15 CDT

dear nicholus

The correct command is

 antechamber -i po4.pdb -fi pdb -o po4.ac -fo ac -c bcc -nc -3

please let us know it worked out.

  

-- 

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>
Date: Thu, 21 May 2009 02:43:37 -0400
Subject: Re: [AMBER] Protein with HETATM, am I doing the

Dear Amit,
                I am with Dr. Parbati Biswas, Reader, Department of
Chemistry, University of Delhi. By the way what type of help can you offer?

On Thu, May 21, 2009 at 1:26 AM, Amit Bajaj <amit_at_dmsystems.in> wrote:

> 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)
> _______________________________________________
> AMBER mailing list
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>

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