AMBER Archive (2005)

Subject: Re: AMBER: Protein with structural ions

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Apr 08 2005 - 11:30:26 CDT

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?

Thank you for your help,

Kara Di Giorgio

On Apr 8, 2005, at 8:41 AM, David A. Case wrote:

> On Thu, Apr 07, 2005, Kara Di Giorgio wrote:
>
>> I'm trying to set distance restraints between some protein sidechains
>> and a structural calcium ion. The calcium leaves its pocket and the
>> protein begins to unravel without any constraints. I made a upb file
>> and tried to use make DIST_RST and got the following error message:
>>
>> makeDIST_RST -upb carestraints.upb -pdb enzph1ala_min3.pdb -rst
>> enzph1ala_rst_min3.rst
>> # makeDIST_RST
>> Currently configured for up to 5000 atoms
>> Using MAP file /usr/local/amber/dat/map.DG-AMBER
>> ERROR no map function for CA CA :data= 79 GLY O 171 CA CA
>> 2.8
>
> Same suggestion as in my last e-mail: use the "raw" sander format,
> described
> in section 5.9. makeDIST_RST is primarily a time-saving front end
> that is
> useful for handling lots of "ordinary" NMR constraints. When you need
> to
> handle things that makeDIST_RST doesn't understand, you should do it
> by hand.
>
> Of course, your final sander input file can include some constraints
> created
> by makeDIST_RST, and others that you wrote yourself.
>
> ...good luck...dac
>
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