[gmx-users] adding NH2 cap to C terminal

[Mark Abraham]

sarbani chattopadhyay wrote:
>   Thank you for reply.
>   Amber  force fields have parameters for C-terminal-C(O)-NH2 . But I 
> don't know which of
> the force fields in Gromacs 3.3.1 have parametrs for the C-terminal 
> amide cap.

Check out the .rtp file. That's how GROMACS knows what it has parameters 
for.

>  Is it
> possible to introduce these parameters manually. What I need to know is 
> that which other
> files  do I need to modify ?

Potentially, none.

> Till now I have only modified the terminal database ,( though I may have 
> made some
> mistake ), but the added "N" 's coordinates are given by pdb2gmx  as " 
> nan nan nan"

Depending on your need, making a custom residue type in the .rtp 
database, or a custom terminus in the .tdb database might work. Either 
way, Chapter 5 is your friend.

Mark