AMBER Archive (2005)

Subject: Re: AMBER: Protein with structural ions

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Sun Apr 10 2005 - 22:05:08 CDT

I've created a .refc file with my four distance restraints in it. I
think I have the correct format. I have figured out I need to add -ref
to the sander command line when I start my simulation.

Right now, I'm not sure how to include the fact that I have distance
restraints in the md.in file. I've tried nmropt =1, nmropt =2 and
nmropt >1 and none of them work. What is the correct flag to use?

Thanks,

Kara Di Giorgio

On Apr 8, 2005, at 10:29 AM, David A. Case wrote:

> On Fri, Apr 08, 2005, Kara Di Giorgio wrote:
>
>> Do you know of any examples I can look at? A problem I have with the
>> Amber manual is that, although I understand the individual parts
>> described, I don't always understand how to put everything together
>> (the format). How is the &rst namelist formatted? How do you
>> incorporate this into your sander command?
>
> There are examples on pp. 169-170 of the Users' Manual. Also, look in
> the
> "nmr" and "rdc" subdirectories under $AMBERHOME/test. And don't
> neglect trial
> and error as a way of figuring out what is going on.
>
> ...dac
>
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