('binary' encoding is not supported, stored as-is)
This is a really simple question, but I am not very familiar with Unix
yet. When I try to edit the define.h file it tells me that it is
read-only. How can I go about editing this file then?
==============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.tbc.com
Homepage: Http://sigyn.compchem.ucsf.edu/members/jmwang/index.html===============================================================
"David A. Case"
<case.scripps.edu
> To
Sent by: amber.scripps.edu
owner-amber.scrip cc
ps.edu
Subject
Re: AMBER: (No subject)
01/29/2004 10:20
PM
Please respond to
amber.scripps.edu
On Thu, Jan 29, 2004, opitz.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.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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