On 5/6/12 2:36 PM, Shima Arasteh wrote:
IS the parameters for a residue in CHARMM36 and CHARMM27 the same?
I would suggest you do a bit of reading about the CHARMM force field hierarchy
and why they are named as they are. If you're parameterizing a new residue you
can do it for either, or both, depending on the parameter set. In your case,
I'd suspect your formyl parameters are going to be universal between CHARMM27
and CHARMM36, but don't let my suggestion be your justification. If a reviewer
asks, "some guy on the Internet said it" is not sufficient justification ;)
-Justin
Thanks in advance,
Shima
--------------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Saturday, May 5, 2012 9:16 PM
*Subject:* Re: [gmx-users] Topology parameters
On 5/5/12 11:39 AM, Shima Arasteh wrote:
> Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27?
>
Maybe, try it and see. Swiss-Param might also be an option.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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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