[gmx-users] terminal residue

Xavier Periole Xavier.Periole at physbio.mssm.edu
Tue Sep 23 19:39:00 CEST 2003

I guess that the best solution would be to create a new residue.
The base could be the lysine and you add your "heteroatom" ch3
bound to nh2. You have to define the topology in ff???.rtp. Choose the
atom type from other residues topology if possible. You have to declare
your new residue by putting it in aminoacids.dat. And probably more
things you'll find out when running grompp.


On Monday, September 22, 2003, at 06:31  am, Lakshmi Padmavathi wrote:

> Dear Gmx users,
>  i want to use a protein along with an heteroatom. the heteroatom is 
> linked to
> the protein. the terminal atom of the heteroatom is ch3. it has to link 
> with
> lysine NH2 ( sidechain).
> i am getting error in pdb2gmx. that c is not fount in 220 residue. 
> which is my
> heteroatom residue number.
> how can i solve this. hetero atom number is 220, and lysine number is 
> 216.
> how will the gromacs recognise the CH3 as terminal.
> can i add this CH3 in ***_c.tdb ?
> could anybody help me regarding this?
> thank you very much in advance.
> sincerely,
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