[gmx-users] adding NH2 cap to C terminal
Mark.Abraham at anu.edu.au
Mon Nov 10 13:05:14 CET 2008
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
> Is it
> possible to introduce these parameters manually. What I need to know is
> that which other
> files do I need to modify ?
> 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.
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