RE: AMBER: Leap adding extra atoms

From: Akshay Patny <akshay17.olemiss.edu>
Date: Thu, 11 Jan 2007 15:38:37 -0600

Thanks Ross

NOTE: I AM USING RESP CHARGE METHOD AND NOT BCC
 
I understand that now. However, I generated the PREP file for my ligand e.g.
DMPC monomer from the input MOL2 ligand file attached. Now, the template
PREP file which is generated has all of atom names different from that of
the input MOL2 file names.

Following are my doubts?

1. Is this change of atom names during PREP file generation occurred because
I used input as MOL2 file?

2. Should I have used PDB as the input file, does using PDB as input file
keep the same atom names in the template PREP file?

3. As for using RESP, I have to use gaussian, the atom name information is
lost during the gaussian job, so should it matter whether to use input file
as MOL2 or PDB??

In any case, my template PREP file which is generated has all of atom names
different from that of the input MOL2 file names, how can I take care of
that now??

Best, I look forward to hear from you.

Akshay (Olemiss)
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
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
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Bill Ross
Sent: Thursday, January 11, 2007 1:33 PM
To: amber.scripps.edu
Subject: Re: AMBER: Leap adding 3 extra atoms

> Loading PDB file: ./telmi_mod.pdb
> Created a new atom named: N5 within residue: .R<TEL 298> <<<==== e.g. N5
> 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> <<<==== e.g. N4
> 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

Notice the atom names. The names in your pdb must match the ones
in your template. Leap cannot determine that e.g. N4 in the
template is the same and N5 in your pdb.

Bill
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Received on Sun Jan 14 2007 - 06:07:35 PST
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