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
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