[gmx-users] error in grompp

Serena Leone sleone at rics.bwh.harvard.edu
Fri Jul 11 20:42:32 CEST 2008

Hi all

I am trying to model a sulfated octasaccharide. I retrieved the 
topology files from prodrg and I fixed them. The same procedure on a 
the monosaccharide unit of the oligosaccharide I'm going to run worked 
smoothly. After solvating the molecule, I try to pre-process it and I 
obtain the following error:

-- Generated 279 of the 1225 non-bonded parameter combinations
WARNING 1 [file "GI.top", line 993]:
  Too few parameters on line (source file toppush.c, line 1168)
processing coordinates...

Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (GI_wb.gro, 17431)
             does not match topology (GI.top, 0)

According to the wiki, the fact that no atom is recognized in the top 
points to an incorrect location of the path for the cpp in the mdp, but 
this is not the case (i double checked, plus this is exactly the same 
mdp file that i used for other runs and that worked fine...). I also 
checked for mispellings of atoms and residues names in the top, but 
everything apparently fits. Do you have any idea of what else may cause 
this behavior?

Thanks a lot

Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586

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