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

Justin Lemkul jalemkul at vt.edu
Sat Sep 8 22:37:16 CEST 2012

On 9/8/12 4:29 PM, Elie M wrote:
> Dear all,
> I am new to GROMACS. I am trying to minimize a structure but first I have to form the pdb file with the correct force field parameters. I am using version 4.0.5 and an OPLSAA force field. The error I am getting is:.......Opening library file /cygdrive/c/Packages/Gromacs/share/gromacs/top/ffOPLSAA-c.tdbProcessing chain 1 (46 atoms, 1 residues)There are 4 donors and 2 acceptorsThere are 0 hydrogen bonds
> -------------------------------------------------------Program pdb2gmx, VERSION 4.0.5Source code file: pdb2gmx.c, line: 429
> Fatal error:Atom C in residue LI 1 not found in rtp entry with 1 atoms             while sorting atoms-------------------------------------------------------
> I read about the error but i could not figure out the "mismatch" that was stated in the input file which you will find attached. Please can anyone help me

The error comes from the fact that pdb2gmx is finding a carbon atom in a residue 
named LI (which is lithium).  Of course, that is nonsense.  Without seeing the 
.pdb file, it's hard to say what's going on, but if you have some residue named 
"LIG" (which will also be unknown to pdb2gmx) then perhaps the format of the 
.pdb file is wrong.  That's just a wild guess though.  But of course, if you 
have "LIG" then you will need to add all the necessary parameters to the .rtp 
file anyway.



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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