AMBER Archive (2008)

Subject: Re: AMBER: molecular structure

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Aug 26 2008 - 17:32:51 CDT

you need to be more specific- what structures are you comparing? how
did you input the structural data to antechamber? how large are the
differences? what is the goal of the simulation? (hard to know if it
will affect it without know what your simulation is designed to study)

On Tue, Aug 26, 2008 at 6:24 PM, Chih-Ying Lin <chihying_at_usc.edu> wrote:
>
>
> Hi
> the bond length, bond angle, dihedral angle determine the molecular structure
>
>
> the bond length, bond angle are easily determined..
> but the dihedral angle are hard to control...
>
>
> I used antechamber to get the set of force field parameters.
> But with that set of the force field parameter, I could not get the exact structure of the molecule (not all of the dihedral
> angles are the same)
>
> will it affect my rest of simulation severely?
>
> Thanks
> Lin
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu