[gmx-users] Centring a protein complex

Justin Lemkul jalemkul at vt.edu
Wed Oct 29 13:22:16 CET 2014

On 10/29/14 8:08 AM, Rohit Farmer wrote:
> Hi Guys,
> I am trying to centre a protein complex using this command
> trjconv -pbc mol -center -ur compact -s em.tpr -f md_0.xtc -o
> md_0_center.xtc
> I selected "protein" in the first option and then "system" in the second
> for output but I received the following error
> Floating point exception1900.000        ->  frame   3000 time
> 30000.000
> I read somewhere that while centring a protein complex its better to select
> one monomer than the whole protein complex. So I tried doing that as well
> by making an index file but I still received the same error. Can someone
> please help me with this.

The floating point exception would suggest that the trajectory is corrupted. 
What does gmxcheck tell you?



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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