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

Justin Lemkul jalemkul at vt.edu
Sat Sep 8 22:50:00 CEST 2012

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:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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