(unknown charset) AMBER: Leap adding 3 extra atoms

From: (unknown charset) Akshay Patny <akshay17.olemiss.edu>
Date: Thu, 11 Jan 2007 11:35:00 -0600

Dear Amber users

I am trying to get TOP and CRD file for an organic ligand telmi.pdb

For that, I have ran antechamber on telmi.pdb using RESP method (the ligand
contains a formal charge of -1).

I have got the following files Telmisartan_charged_frcmod and
Telmisartan_charged_resp.prep

Now, I am using these files in Tleap:

% $AMBERHOME/exe/tleap -s -f leaprc.ff99
Tleap> source leaprc.gaff
Tleap> loadamberprep Telmisartan_charged_resp.prep
Tleap> loadamberparams Telmisartan_charged_frcmod

Now, when I do

Tleap> check TEL
It gives following output >>>>

Checking 'TEL'....
WARNING: The unperturbed charge of the unit: 0.999960 is not zero.
Checking parameters for unit 'TEL'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.

Now when I try to load my ligand PDB file, it gives following >>>

> jip = loadpdb telmi_mod.pdb

Loading PDB file: ./telmi_mod.pdb
Created a new atom named: N5 within residue: .R<TEL 298>
Created a new atom named: C35 within residue: .R<TEL 298>
Created a new atom named: O3 within residue: .R<TEL 298>
  Added missing heavy atom: .R<TEL 298>.A<O2 60>
  Added missing heavy atom: .R<TEL 298>.A<N4 42>
  Added missing heavy atom: .R<TEL 298>.A<C33 25>
  total atoms in file: 39
  Leap added 32 missing atoms according to residue templates:
       3 Heavy
       29 H / lone pairs
  The file contained 3 atoms not in residue templates

PS: I DO NOT UNDERSTAND WHY IS IT ADDING 3 HEAVY ATOMS TO THE FILE, CAN YOU
SUGGEST HOW TO FIX THIS PROBLEM. I SAVED THE OUTPUT PDB AND HAVE ATTACHED IT
HERE AS telmi_amber.pdb

Best regards
Akshay (Olemiss)
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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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Received on Sun Jan 14 2007 - 06:07:29 PST
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