[Dock-fans] Error creating gaff.mol2

[teck maan lim]

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
>
>
>