[gmx-users] Incorrect bond in top file

Justin Lemkul jalemkul at vt.edu
Mon Aug 27 21:47:32 CEST 2012

On 8/27/12 3:03 PM, Shima Arasteh wrote:
> OK, I checked the bonds section of top, there  is no bond between CN and HN.
> Thanks for it.
> But there is a new problem.
> I passed the steps for simulation the protein in water, up to the EM step. I ran grompp and then mdrun to do energy minimization. I see the protein broken. As you said in another email asked a few hours ago, I ran the command trjconv :
> # trjconv -s EM.tpr -f EM.gro -pbc mol -ur compact -o EM_pbc.gro
> I still see the protein broken.The FVAL is not connected to the next residue. Would you let me know your idea? Is there any trick here?

Your .rtp entry needs a bond between the C of FVAL and the N of the next 
residue, i.e.:

C +N

in the [bonds] directive.

Again, in general, be advised that nothing you see in visualization software is 
definitive; only the topology is.  In this case, going back to your .rtp entry, 
I suspect that the bond is, in fact, absent.



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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