[gmx-users] question

[Andrew Bostick]

Dear Justin

Very thanks for your answer

I should use my pdb file in which there is no bond between CD atom of GLU
residue from peptide 1 and NZ atom of LYS residue from peptide 2. Creating
new entry in specbond.dat file will consider this new bond. Is my vision
true?

Based on your answer, only thing I should do is creating a new entry in
specbond.dat? Should I don't other thing?

Based on following link (
http://www.gromacs.org/Documentation/File_Formats/specbond.dat), my new
entry is as follows, is it true?

GLU     CD      1       LYS     NZ      1       0.13     GLU2    LYS2

How to get the  accurate reference length for searching for candidate bonds?

In my system there is more than 1 Lys and 1 Glu residues. I want this new
bond between special residue of  Lys (for example number: 28 ) and special
residue of Glu (for example number: 45). How to set this state in
specbond.dat file?

I am beginner in this field. Please guide me about that.

Thanks in advance.