AMBER Archive (2009)

Subject: RE: [AMBER] convert .mol2 file to .pdb with atomtype definitions

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Tue Mar 17 2009 - 11:41:20 CDT

Hey Pansy

Perhaps you could try PYMOL. If your mol2 file has proper residue names,
PYMOL gives you acceptable pdb file. However, pymol may consider all
residues as HETATM, which you may want to convert to ATOM.

Hope this helps

Cheers

PanDa

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If your ship doesn't come in, swim out to it...Jonathan Winters
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Pankaj R. Daga                 | 
Dept. of Medicinal Chemistry  |  e-mail:  pdaga_at_olemiss.edu
417 Faser Hall, |  fax:          +1-662-915-5638
University of Mississippi      |  phone:        +1-662-915-1853
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-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of Pansy Patel
Sent: Tuesday, March 17, 2009 11:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions

Hello David

"Have you tried using LEaP: use loadmol2 followed by savepdb? You may
have to do some experimentation and hand editing (either of the input or
output file), but it may get you close."

Yes I tried that too
and this is the error i get

Loading PDB file: ./GC-hexamer.pdb
-- residue 1: duplicate [ C] atoms (total 114)
-- residue 1: duplicate [ H] atoms (total 136)
-- residue 1: duplicate [ N] atoms (total 48)
-- residue 1: duplicate [ O] atoms (total 68)
-- residue 1: duplicate [ P] atoms (total 10)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Unknown residue: RES number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: RES sequence: 1
Created a new atom named: O within residue: .R<RES 1>
Created a new atom named: C within residue: .R<RES 1>
Created a new atom named: N within residue: .R<RES 1>
Created a new atom named: H within residue: .R<RES 1>
Created a new atom named: P within residue: .R<RES 1>
Bond: Maximum coordination exceeded on .R<RES 1>.A<H 4>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<RES 1>.A<C 2> .R<RES 1>.A<H 4>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found
!
!ABORTING.

Is there any module on amber which can add atomtypes to the existing pdb
file

Pansy

>>> "David A. Case" <case_at_biomaps.rutgers.edu> 3/17/2009 12:00 PM >>>
On Tue, Mar 17, 2009, Pansy Patel wrote:
>
> I would like to convert a .mol2 file into a .pdb file.
> The 'antechamber' in Amber is designed to convert single residues.
> My file is a DNA structure model in .mol2 format with another small
organic molecule interacting with it.
> I tried to use babel to convert the file
> but all the atoms are termed RES which is not the right atom type
> Is there some way that I can generate atom types for the DNA part of the
mol2 file using amber or any other accessible software ?
>

Have you tried using LEaP: use loadmol2 followed by savepdb? You may
have to do some experimentation and hand editing (either of the input or
output file), but it may get you close.

....dac

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