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

Elie M elie.moujaes at hotmail.co.uk
Sat Sep 8 22:46:59 CEST 2012

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)..

Thanks once again

> Date: Sat, 8 Sep 2012 16:37:16 -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 4:29 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
> -- 
> ========================================
> 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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