[Dock-fans] Error creating gaff.mol2

Greg Warren greg at eyesopen.com
Mon Jun 2 13:56:51 PDT 2008


Hi Teck,

If you have an OpenEye license then there is an application that is 
license to academic users for file conversion.  The application is 
Babel.  It requires a OEChem license like convert.py.  The process would 
look like

babel -in my_molecule.cdx -out my_molecule.mol2

If you are input a 2-D chemdraw structure you will get a z coordinate 
column with only zeros.

Regards,

Greg

teck maan lim wrote:
> Hi,
> I tried to write a mol2 file from chemdraw, but i still have same 
> problem in the amber score. I tried convert.py but it is missing a 
> module in it. Is there a free GUI program that you all use to create a 
> mol2 that can be used in amber score? Thanks
>
> Teck Maan
>
> Scott Brozell wrote:
>   
>> Hi,
>>
>> I am not a chemdraw user, but it seems likely one can write a
>> mol2 file from it.
>>
>> On Thu, 29 May 2008, John J. Irwin wrote:
>>
>>   
>>     
>>> hmmm. why not use convert.py from OEChem?
>>>
>>>
>>> Teck Maan wrote:
>>>     
>>>       
>>>> I made a ligand in chemdraw and would like to convert them into mol2
>>>> format using openbabel so that i could run a amber score on onto a pdb
>>>> file. But i run into this syntax error saying that (Multiple '.' in
>>>> NUMBER-like thing (5.1.gaff.mol2)). Below is the log. 
>>>>
>>>> log started: Thu May 29 13:14:34 2008
>>>>
>>>> Log file: ./leap.log
>>>>   
>>>>       
>>>>         
>>>>>  # LEaP called by /home/tkmaan/Desktop/dock6/bin/amberize_ligand
>>>>>  source leaprc.gaff
>>>>>         
>>>>>           
>> ...
>>   
>>     
>>>>>> gaff = loadamberparams gaff.dat
>>>>>>       
>>>>>>           
>>>>>>             
>>>> Loading
>>>> parameters: /home/tkmaan/Desktop/dock6/parameters/leap/parm/gaff.dat
>>>> Reading title:
>>>> AMBER General Force Field for organic mol., add. info. at the end (June,
>>>> 2003)
>>>>   
>>>>       
>>>>         
>>>>>  # Begin DOCK Amber Score ligand specific processing
>>>>>  frcmod=loadamberparams 5.1.frcmod
>>>>>     
>>>>>         
>>>>>           
>>>> (Multiple '.' in NUMBER-like thing (5.1.frcmod))
>>>> Could not open file 5.1.frcmod: not found
>>>>       
>>>>         
>> ...
>>   
>>     
>>>>>  5.1=loadmol2 5.1.gaff.mol2
>>>>>         
>>>>>           
>>>> ERROR: syntax error
>>>> (Multiple '.' in NUMBER-like thing (5.1.gaff.mol2))
>>>>   
>>>>       
>>>>         
>>>>>  check 5.1
>>>>>         
>>>>>           
>>>> ERROR: syntax error
>>>>   
>>>>       
>>>>         
>>>>>  savepdb 5.1 5.1.amber.pdb
>>>>>         
>>>>>           
>>>> ERROR: syntax error
>>>> (Multiple '.' in NUMBER-like thing (5.1.amber.pdb))
>>>>   
>>>>       
>>>>         
>>>>>  saveamberparm 5.1 5.1.prmtop 5.1.inpcrd
>>>>>         
>>>>>           
>>>> ERROR: syntax error
>>>> (Multiple '.' in NUMBER-like thing (5.1.prmtop))
>>>> (Multiple '.' in NUMBER-like thing (5.1.inpcrd))
>>>>       
>>>>         
>> There is a pattern here.
>> 5.1 is not a valid LEaP variable name.
>> Name your ligand mol2 files with alphanumeric strings that
>> start with an alphabetic character.
>> See section 3.2.2
>> http://amber.scripps.edu/doc9/index.html
>>
>> Scott
>>
>>
>>   
>>     
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>   

-- 
========================================
Gregory Warren, PhD
Senior Applications Scientist
CEAPAS
OpenEye Scientific Software, Inc
9 Bisbee Court, Suite D
Santa Fe, NM 87508
(505) 473-7385 ext 50
mailto:greg at eyesopen.com
========================================

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