[gmx-users] terminal residue

[Anton Feenstra]

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 ?

For this, your heteroatom must be recogniszed as part of the protein. It may
be easiest to build a modified Lysine residue that contains this atom already
bonded to it. For this, you will have to make an new entry in the .rtp file
for your modified lysine (with a new name), add it also to aminoacids.dat, and
if you need atomated generation of hydrogens, make a corresponding .hdb entry.
Also, in your input file (.pdb presumably), the heteroatom must be placed
right after the lysine.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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