[gmx-users] Re: gmx-users Digest, Vol 85, Issue 114

[Gerrit Groenhof]

> 
>   3. QMMM+NMA (Yao Yao)
>   
> Hi Gmxers,
> 
> I am wondering if NMA has been introduced into QMMM part of gromacs.
> I am trying to get vibrational frequencies of proteins by normal mode analysis (NMA) in the framework of QMMM.

This is not possible, unless your system is so small that you can evaluate the hessian numerically.

Gerrit


> 
> Thanks,
> 
> Yao 
> 
> vang3 at gmail.com>
> Subject: Re: [gmx-users] about side chain and structure rifinement
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTikhcJ_EnVjHKLzffnk5DRKedVBguQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> A MM ff like OPLS will probably do your job. However CASP experiments show
> that knowledge-based potentials like the one Rosetta implements, produce
> more physically realistic results. If you only want to improve the
> side-chain conformations, I'd suggest to use a program that employs rotamer
> libraries like SCWRL4.
> 
> 
> On 17 May 2011 12:05, marco miele <marco.miele75 at gmail.com> wrote:
> 
>> Hi everyone
>> My question is that I have a receptor protein modeled which have some
>> problem with side chain angles, I would like to know if is good to
>> apply OPLS ff in vacuum to improve the side chain in particularly and
>> structure in general.
>> what you suggest me.
>> Cheer marco
>> --
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> 
> 
> 
> -- 
> 
> ======================================================================
> 
> Thomas Evangelidis
> 
> PhD student
> 
> Biomedical Research Foundation, Academy of Athens
> 
> 4 Soranou Ephessiou , 115 27 Athens, Greece
> 
> email: tevang at bioacademy.gr
> 
>          tevang3 at gmail.com
> 
> 
> website: https://sites.google.com/site/thomasevangelidishomepage/
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> End of gmx-users Digest, Vol 85, Issue 114
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