[gmx-users] error in producing top file for a structure

[Elie M]

Thanks very much for the help. I will see what I can do about that.
Sincerely
ELie

> Date: Sat, 8 Sep 2012 16:50:00 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] error in producing top file for a structure
> 
> 
> 
> On 9/8/12 4:46 PM, Elie M wrote:
> >
> >
> > Thanks a lot for your response. Actually i do have LIG , which obviosuly the
> > code did not understand and changed it into LI; at first I thought LI was LIG
> > but in GROMACS' language. Is there any place where I can read how to
> > implement changes in the .rtp file? or any other way to get the correct pdb
> > format. i used openbabel because Markin SKETCH and ArgusLAB do not seem to
> > keep the charged Nitrogen and Chlorine ions I have got in my structure. By
> > the way, I have attached the pdb input file (I guess)..
> >
> 
> The list does not accept attachments.  If Gromacs is interpreting "LIG" as "LI" 
> then the .pdb file is formatted incorrectly - at least one column is shifted, 
> which will lead to misinterpretation of all of the contents.  If you want to add 
> a new residue in the .rtp file, refer to the manual, section 5.6.1, in 
> conjunction with implementation details at:
> 
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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