AMBER Archive (2009)

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

From: Wei Zhang (wei.zhang_at_uth.tmc.edu)
Date: Tue Mar 17 2009 - 11:33:27 CDT

Hi Pansy,

     LEaP can only assign atom type for standard residues (protein,
DNA, RNA).
It can not handle non-standard residues (in your case residue: RES)
directly.
What you have to do is:

1. save the residue RES in a separate file,

2. use antechamber to prepare a mol2 format file which contain the
correct amber atom type
      for residue RES

3. in LEaP load the new mol2 file first, then load the whole pdb file.

then you can save the whole thing in a full mol2 file which has the
correct atom types for all atoms.

Sincerely,

Wei

On Mar 17, 2009, at 11:09 AM, Pansy Patel wrote:

> 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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