[gmx-users] error NH2 in C terminal

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 2 11:49:58 CEST 2008

shahrbanoo karbalaee wrote:
> Dear Justin
> Thank you for your advice.
> there is NH2 in c terminal  sequence peptide  but when I do pdb2gmx I
> get error.I delete NH2  by hand and do pdb2gmx -f  name.pdb -ter  and
> choose none in c terminal .when I see top file I see NH2 add in C
> terminal.Is it correct?

I don't understand how deleting NH2 is causing it to show up in the topology.

> and  another  way I use missing in command pdb2gmx .I get top file
> similar to first top(according  delet NH2).Please advise me,what is
> differnce top files  with  two way and which one is  better I choose?

Never use a topology that has missing atoms.

What might be better is if you could paste the end of your .pdb file (showing 
the last residue with NH2, and the corresponding pdb2gmx command lines, then any 
modifications you have tried.  Right now I do not understand what you are doing.


> thanks again


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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