[gmx-users] trouble adding c-terminal formyl group to ff*.rtp

Senthil Kandasamy senthilk at umich.edu
Thu Oct 9 00:25:01 CEST 2003

Hi gmx-users, 

I am trying to add a formyl group to the c-terminus and a ethanolamine
group to the n-terminus of a WALP peptide. Both are uncommon residues
and are not present in the residue or termini database. Based on
previous suggestions for  other uncommon residues, I added the groups
FOR and ETA to the ffg*.rtp (rather than mess with the tdb file). That
seemed fine.

I also added the appropriate entries to the hydrogen data base. I am
running into some problems here. I was able to add the two hydrogens for
the N-terminal ethanolamine group


without problems.

However, for the C-terminal formyl group, 


I need to define a dihedral that involves the N atom of the "next"
aminoacid. How do I incorporate this into the hdb file? (As I
understand, the "previous carbon " can be designated as a -C.) 

(Thought: Am I better off defining the C-terminal formyl group in the
tdb file?)

I am a little confused here.

Hope some one can throw some light on this 



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