AMBER Archive (2004)

Subject: Re: AMBER: (No subject)

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Fri Jan 30 2004 - 10:31:10 CST

You have to make sure that you have write rights:

chmod +w filename

and that you are the owner of the file (it might be that the owner of
that file is root and then you have to login as root)

Usually a good ideea is if you want to modify the code is to compile the
a copy of the program in your home directory and then use it as you need.
Hope this helps
vlad

opitz_at_che.udel.edu wrote:

>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_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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-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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