[gmx-users] Generating topology for a hem protein

Justin Lemkul jalemkul at vt.edu
Thu May 19 15:46:19 CEST 2016

On 5/19/16 9:41 AM, zeineb SI CHAIB wrote:
> Dear all,
> I'm desperetly looking for help to generate the topology of my hem protein.
>    I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals
> that should not exist and it's complicated to verify everything. Justin
> suggested using CHARMM-GUI, I followed a tutorial that I found on line
> (http://cermm.concordia.ca/workshopDocs/CHARMM/Lague.pdf) in order to build
> my system, I'm in the final step, adding the Hem group to my protein but I
> don't know how to do it and I don't know if all the steps went well or not.

If you don't know, how can anyone on this list know?  If something went wrong 
with CHARMM-GUI, there would be a fatal error.  It's as simple as uploading the 
PDB file and letting CHARMM-GUI do the work; our latest version even writes all 
the GROMACS topologies and input files for you.  It will generate the correct 
dihedrals for heme groups.

Unless you can provide a specific issue (with GROMACS, because this is not the 
place for CHARMM-GUI problems), there's nothing anyone can do to help you.  We 
can't guess what the problem is, and in this instance, you haven't even said if 
there is a problem.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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