[gmx-users] endcapping

[w.j.schravendijk at students.pharm.uu.nl]

Dear Gromacs users,

I would like to test an endcapped 26 residue-peptide. The carboxyl
end-group is amidated: C(O)NH2 instead of C(O)OH.

In the pdb file, the amide group is mentioned as an extra residue and
looks something like this:

HETATM  201  N   NH2 A  27      13.279   5.297  18.956  1.00 48.71
TER     202      NH2 A  27

pdb2gmx gives the error: no alpha carbon present in residue 27.

How should I proceed? I guess there are several options:
- create an extra NH2 entry in the n-termini database ffgmx.tdb
- create an extra residue in the residue database, resembling my
end-capped residue.
- remove the NH2 residue from the pdb file and try to put it back after
pdb2gmx by editing the .top and .gro file. However, how do I check if the
edited topology and coordinate file are correct?

I would also like to label that residue, I guess that requires the same
steps?

Greetings, Pim