AMBER Archive (2009)

Subject: Re: [AMBER] Regarding rigid bond

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 01 2009 - 05:28:58 CST

the only option is to constrain all bonds. you cannot do this for some bonds
and not for others unless you modify the code (which is not possible unless
you have programming experience).

Dear Prof. Carlos,
> Thanks for your immediate reply. In my case, system contains three
> different kinds of molecules and I am using United Atom model for molecule
> No.-1 ( parameters from literature where all bonds were treated as rigid).
> How can I keep these type of bond rigidity in Amber. I am using Amber 9.0
> version.
>
> Thanks in advance
>
> Regards
> Aneesh
>
> On Fri, Nov 27, 2009 at 11:54 PM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
> > Check the NTC variable options in the manual
> >
> >
> > On Nov 27, 2009, at 12:29 PM, aneesh cna <aneeshcna_at_gmail.com> wrote:
> >
> > Dear amber users,
> >>
> >> I am using Amber 9.0 version. I would like to keep rigid
> >> bonds in the molecule under study during the simulation. How can I
> >> implement
> >> this in Amber?. Waiting for your reply
> >>
> >> Thanks in advance
> >> Aneesh
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