AMBER Archive (2009)

Subject: Re: [AMBER] Inquiries about antechamber

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Wed Aug 26 2009 - 16:02:21 CDT

Dear Yikan,

I have a question: Does the TMS residue that you mentioned in your e-
mail consist of the HETATOM entries in your PDB? If I am looking at
it right, the PDB contains a nucleic acid, and it should be one large,
covalently-bonded molecule, correct?

Remember, antechamber can handle only one species (covalently bonded
molecule) at a time. If your TMS residue should be part of the
nucleic acid, why are they listed as HETATOM? I don't know whether
antechamber distinguishes between ATOM and HETATOM entries in a PDB
(the way CDCC Mercury does, see attached PNG file), but I think this
is a bit confusing. Probably a result of the software used to
generate the PDB.

The other issue is that your PDB file lists two MODELS, with very
similar coordinates (see lines that contain "MODEL 1" and
"MODEL 2"). Maybe you could try cleaning up this PDB file, and
then sending it to antechamber?

Good luck!

Nick Musolino



---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528

On Aug 26, 2009, at 1:07 PM, Yikan Chen wrote:

> Hey,
> I have downloaded a pdb file from www.rcsb.org, as shown in the
> attachment
> (1X6W.pdb).
> It cannot be regonized by Amber force fields directly because there
> is a
> TMS residue that is not included in any force field. So I use
> antechamber to
> generate a new pdb file and run it in Gaff. It goes like follows:
> $AMBERHOME/exe/antechamber -i 1X6W_3.pdb -fi pdb -o newff.pdb -fo pdb
> And 1X6W_3.pdb is revised pdb file for antechamber. There are error
> messages like the following:
>
> Unrecognized atomic name JB, exit
> Unrecognized atomic name JB, exit
> Unrecognized atomic name JA, exit
> For atom[28]:E2, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[29]:GA, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[30]:GB, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[31]:GC, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[32]:A1TT, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[33]:B1TT, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[38]:E3, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[41]:B6, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[42]:B7, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[46]:JB, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[47]:JA, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[48]:KA, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[49]:KB, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[50]:LB, the best APS is not zero, bonds involved by this
> atom are
> frozen
> For atom[51]:LA, the best APS is not zero, bonds involved by this
> atom are
> frozen
> ---Judge bond type for Residue 1 with ID of 1 and Name of S ---
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic
> double)Error: cannot run
> "/itc/apps/amber/10/amber10/bin/bin.Linux.x86_64/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
>
> What is that problem? It really puzzles me!
> Thank you very much!
>
> Best,
> Yikan
> <1X6W.pdb><1X6W_3.pdb>_______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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