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.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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Received on Wed Mar 18 2009 - 01:17:15 PDT
