[Dock-fans] Re: Dock-fans Digest, Vol 13, Issue 20

Terry Lang terry at cgl.ucsf.edu
Wed Aug 10 17:23:35 PDT 2005


Dear Jose,

          The minimum format you need for properly reading the mol2 file 
into sphere_selector is below. 

@<TRIPOS>MOLECULE
benzene
12 12 1 0 0

@<TRIPOS>ATOM

"benzene" can be replaced with the name of your molecule or atom or can 
be blank, but there must be at least a newline between @<TRIPOS>MOLECULE 
and the number line.  The number line contains values for:

# of atoms   # of bonds   # of substructure entries    # of features    
# of sets

It does not matter how many other lines are between the number line and 
the @<TRIPOS>ATOM line, and you do not need the @<TRIPOS>SUBSTRUCTURE 
entry. 

Good luck and let me know if you are still having problems,
Terry



Jose A wrote:

>Dear Oshik:
>
>I had the same problem you have described so far with spehere selector
>and got mine to run properly. In my case, I had forgotten to include a
>header (and footer?) to the mol2 file I was trying to use.
>
>basically I had the a single line for a single atom guiding the
>selction of spheres. I opened up a random mol2 file from another file
>and copied and pasted everything from "@<tripos>molecule" to
>"@<tripos>atom" as a header, and on the bottom I threw in the
>@<tripos>substructure line (and the one one following that) as a
>"footer". I am not sure everything I beefed up the mol2 file with is
>necessary, but this gave me the results I wanted. If anybody else
>cares to elaborate on this, we will be grateful...what is the minimum
>header(footer?) nesessary for sphere selector to work properly?
>
>hope this solves your problem Oshik,
>
>Jose
>  
>
>>------------------------------
>>
>>Message: 3
>>Date: Wed, 27 Jul 2005 20:51:47 -0700
>>From: Terry Lang <terry at cgl.ucsf.edu>
>>Subject: Re: [Dock-fans] sphere_selector problems
>>To: oshikseg at post.tau.ac.il
>>Cc: 'dock-fans' <dock-fans at docking.org>
>>Message-ID: <42E85653.6040902 at cgl.ucsf.edu>
>>Content-Type: text/plain; charset=windows-1255; format=flowed
>>
>>Dear Oshik,
>>
>>        There are several things that may be wrong:
>>
>>1)  sphere_selector may not be working on your operating system for some
>>reason.  You can test this by running the demo.
>>2)  there is something wrong with the format of your files
>>3)  there is something wrong the code
>>
>>If the problem is 2 or 3, then you will need to send me your files so I
>>can diagnose the issue.  It is a bit difficult to provide more
>>information based on what you have posted so far.
>>
>>Good luck,
>>Terry
>>
>>oshikseg at post.tau.ac.il wrote:
>>
>>    
>>
>>>hello!
>>>I am still having  problems with the "sphere_selector" program. I give the right
>>>input files in the right order but I still  don't get any output file.
>>>I will be grateful if you can send me two files (.sph &.mol2 ) so that i can
>>>check the program itself.
>>>
>>>Sincerely
>>>oshik segev
>>>      
>>>
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>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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