AMBER Archive (2004)

Subject: Re: AMBER: (No subject)

From: opitz_at_che.udel.edu
Date: Fri Jan 30 2004 - 15:32:01 CST

('binary' encoding is not supported, stored as-is) After changing the MAXATOM in define.h, it still crashes at the same atom
number 512. Do I need to recompile it, retest it, or do anything else to
it? Or is there some other value I need to change too? Thanks,

Armin

==============Original message text===============
On Fri, 30 Jan 2004 10:02:50 EST Junmei Wang wrote:

For the antechamber in amber7, you may change the MAXATOM in define.h to
extend the array sizes. The latest version of antechamber in amber8 can
automatically extend the array sizes and should greatly reduce the crashes.
However, it is still recommended not to try very large molecules, such as
molecules having more than 1000 atoms . In the latest version of
antechamber, a function is called to check the atom name duplication.

Thanks

Junmei
===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html===============================================================

                                                                           
             "David A. Case"
             <case_at_scripps.edu
> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       Re: AMBER: (No subject)
             01/29/2004 10:20
             PM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

On Thu, Jan 29, 2004, opitz_at_che.udel.edu wrote:
>
> I am trying to read a pdb file into antechamber. Smaller files work find
> and I get the prepin file etc. etc. A larger file I have that I need to
> put into antechamber, it crashes. Here is the command and following error
> message I get:
>
> antechamber -i file.pdb -fi pdb -o file.prepin -fo prepi -s 2
>
> Unrecognized atomic name , exitSegmentation fault (cored dumped)
>
> Here ist the first few lines of the pdb file then continued around the
> number of atoms where the crash usually happens (atom 513):
>
> ATOM 4 N UNK 1 2.794 -5.632 1.628 1.00 0.00
> ATOM 5 H UNK 1 2.867 -6.567 1.339 1.00 0.00
> ATOM 6 C UNK 1 -2.310 -3.184 2.662 1.00 0.00
> ATOM 7 H UNK 1 -1.466 -3.777 2.913 1.00 0.00
> ATOM 8 H UNK 1 -2.077 -2.575 1.805 1.00 0.00
> ATOM 9 C UNK 1 -2.660 -2.297 3.964 1.00 0.00
> ATOM 10 H UNK 1 -1.875 -2.246 4.622 1.00 0.00

Atom names within a residue must be unique; you cannot just label things
"N", "C", "H", etc. Also, while I don't know the upper limit of atoms,
513 is probably too many. Antechamber was designed to be used for
relatively
small molecules. [Still, it should not crash.....]

We will look into this sort of problem, to see if we can reproduce and fix
it.

..thanks...dac 

--

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:
La Jolla CA 92037  USA            |    http://www.scripps.edu/case==================================================================
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