[gmx-users] RENUMTOP

[David]

On Sun, 2004-02-15 at 08:14, Martina Bertsch, PhD wrote:

> > The simplest test for your topology is to minimize the ligand separately
> > of the protein, and in the process get rid of possible error in your
> > ligand top.
> No, there is no line number in the error message.
> 
> My ligand resembles tryptophan a little bit, so I borrowed some
> ffG43a1 parameters for Trp. I will try minimizing the ligand itself.
> But, is there anything wrong with the format of my lig_vac.itp? 
> > > 
> > > 
> > > Best regards,
> > > Martina Bertsch, Ph.D.
> > > 
> > >  [ moleculetype ]
> > >  ;name nrexcl
> > > DRG      3
> > > [ atoms ]
> > > ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> > > typeB    chargeB     massB
> > >     1m       CH3     285   DRG     CAO      1       0.000    15.035
> > >     2m         C     285   DRG     CAM      1       0.380    12.011
> > >     3m         O     285   DRG     OAN      1      -0.380   15.9994
> > >     4m         N     285   DRG     NAL      2      -0.280   14.0067
          ^^^
where do those m's come from? grompp wants simple numbers from 1 to N
here.


If you have that everything should work without renumbering...

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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