Sai Pooja wrote:
Would it be possible to add some capping residues (like --COCH3 and
--NHCH3) by writing a separate .itp file and including it in the
topology file? Is there a way to make it consistent with charmm forcefield?
No, because you have to specify bonds between these capping residues and your
protein. If you're #including them as new [moleculetypes], then you can't add
these bonds.
Can this be done alternatively by modifying the .rtp file? If yes, what
other operations must one do before using these .rtp files?
Reading in the manual about the file format? I don't understand your question
entirely. All the other force fields use .rtp entries for caps, so I don't see
why this couldn't be done.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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