---------------------------------------------------------------------------
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>_______________________________________________
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