Hi Marcelo,
You cannot run MD if there are missing parameters for your system. Just “freezing” some of the atoms will not work.
What I’d suggest is that, if parameters are not available, you should try to generate the missing parameters by using one of the many available methods. The choice of the specific method you use may depend on your system. With more details, some people on this list may be able to help you choose.
Gustavo Seabra
> Em 21/09/2015, à(s) 16:21, Marcelo Andrade Chagas <andrade.mchagas.gmail.com> escreveu:
>
> Dear AMBER of the list,
>
> how to freeze atoms in an active site of a protein
> that do not have parameters and perform an MD ???
>
> Best regards
>
> Marcelo
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
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Received on Mon Sep 21 2015 - 13:00:03 PDT
