[gmx-users] grompp erro

Justin Lemkul jalemkul at vt.edu
Sun Jan 19 17:43:54 CET 2014

On 1/19/14, 11:37 AM, Albert wrote:
> On 01/19/2014 05:23 PM, Justin Lemkul wrote:
>> Google knows about dozens of posts about this error.  The list is archived for
>> a reason!
>> -Justin
> Hello Justin:
> thanks for the reply. I've already looked into previous thread. It seems that
> this error comes from merge.rtp.

The error comes (more or less) from ffbonded.itp, because grompp is looking 
through your topology for all the bonded interactions it needs, and in this 
case, can't find one.

> I am using latest 2014 charmm36 for my system. I've introduced two HISD and one
> GLUP residues for my protein (I specified them in the input.pdb file when I am
> doing pdb2gmx). when I tried to do minimization with the pdb2gmx output file,
> the above error occurs. However, if I don't introduced the the above three
> residues, there is not any problem.....
> I don't know what happen to the HISD and GLUP residue parameters in the latest
> 2014 charmm36 FF..

All of this is critical information that you left out of your original post, 
hence my assumption that your issue could be easily solved.  When reporting a 
problem, please be as specific as possible!  If there is a problem with our 
latest parameters, we need to fix that, but I don't yet have enough information 
to tell you what's wrong.  grompp did, however, give you what you need to figure 
it out.  The fatal error comes from line 23560 of the topology file.  What is on 
that line?  What are those atoms and what are their types?



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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