[gmx-users] Topology parameters

[Shima Arasteh]

All right. 

Thank you so much.
Shima



________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, May 6, 2012 11:32 PM
Subject: Re: [gmx-users] Topology parameters
 


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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *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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