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.
-Justin
thanks again
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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