Bernhard Knapp wrote:
Hi there,
I wanted to ask if gromacs is able to deal correctly with peptides which
have been acetylized at the N-terminal end? if so what would be the
approbriate way (tool) to model the acetyl?
Various force fields have the acetyl group available as an N-terminal
"capping" group. As such, you still follow the same general procedure
with pdb2gmx to generate the topology, but the .rtp file needs (say) an
"ACE" entry and in the structure file the acetyl atoms need to have a
residue name that matches the .rtp file entry.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
