AMBER Archive (2004)

Subject: Re: AMBER: (No subject)

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 29 2004 - 22:20:43 CST

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 

-- 

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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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