AMBER Archive (2009)

Subject: Re: [AMBER] Inquiries about antechamber

From: Yikan Chen (yc2r_at_virginia.edu)
Date: Wed Aug 26 2009 - 21:05:40 CDT

Hi Nick,
  Thank you for your reply!
  I think TMS residue shuold be a part of the nucleic acid and I have
already changed all of these HETATOM into ATOM in 1X6W_3.pdb. Also, there
was 2 models in 1X6W.pdb and I deleted one of them in 1X6W_3.pdb. Still that
1X6W_3.pdb cannot be recoginized by antechamber.
  Any suggestions?

  Best,
  Yikan

On Thu, Aug 27, 2009 at 5:02 AM, Nicholas Musolino <musolino_at_mit.edu> wrote:

> 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<http://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
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber