Dear Yikan,
maybe you can try to use Gassain03 to calculate the charge of your special
atoms, then with these charges and your cordination, you can use the
antechamber to calculate again.
but remember to calculate with HF/6-31G, then with BLYP.
GOOD LUCK!
zhenhui jackie
2009/8/26 Nicholas Musolino <musolino.mit.edu>
> 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.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.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Sep 02 2009 - 23:05:41 PDT
