[Dock-fans] Error creating gaff.mol2

[Scott Brozell]

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