[gmx-users] include new residues in the rtp file

Marcela P.Aliste marcela.aliste at biology.gatech.edu
Fri Jun 18 21:05:32 CEST 2004

Hi :

I added new residues in the ffG43a2.rtp file and included in the 
aminoacid.dat and in
the ffG43a2.hdb. This new residues are for the N-terminal and the 
C-terminal part of 12 separated alpha helices.
I did this before with no problem to run distances restraint between 
the different helices.

I modified some of the helices and include the new n and c-terminal.
I got the following problem using pdb2gmx in the new structures

Fatal error: Atom O in residue LEC 21 not found in rtp entry with 10 
atoms	while sorting atoms.
I checked : the name, the number and order of the atoms in the pdb and 
in the rtp.

This residue is the last one in the first helices.
I modified and included these residues in the aminaocid.dat ffG43a2.rtp 
and in the ffG443a2.hdb

Is there another file to modify?
Could be the problem that is trying to connect the last residue with 
the first of the next helix?
Thanks a lot
Marcela P. Aliste

Dr. Marcela P. Aliste
School of Biology
Georgia Institute of Technology
310 Ferst Dr.
Atlanta, GA 30332-0230

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