[Dock-fans] Re: Dock-fans Digest, Vol 13, Issue 20
terry at cgl.ucsf.edu
Wed Aug 10 17:23:35 PDT 2005
The minimum format you need for properly reading the mol2 file
into sphere_selector is below.
12 12 1 0 0
"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
Good luck and let me know if you are still having problems,
Jose A wrote:
>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,
>>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
>> 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.
>>oshikseg at post.tau.ac.il wrote:
>>>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.
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>Dock-fans at docking.org
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
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