AMBER Archive (2006)

Subject: AMBER: xleap problem and answer

From: Thomas Pochapsky (pochapsk_at_brandeis.edu)
Date: Wed May 31 2006 - 13:32:32 CDT

Thanks, Dave, I am forwarding this to the reflector for anybody who
is interested; the problem was that everything was correctly defined
in the frcmod file except the non-bonded radius of OL and NL; once
those were defined the problem goes away.

Tom Pochapsky

Begin forwarded message:

> From: "David A. Case" <case_at_scripps.edu>
> Date: May 30, 2006 7:55:15 PM EDT
> To: Thomas Pochapsky <pochapsk_at_brandeis.edu>
> Subject: Re: maybe a simple question?
>
> On Tue, May 30, 2006, Thomas Pochapsky wrote:
>
>> Hi, Dave, I am in my usual bi-annual need to use AMBER for something
>> mode; as always I have to relearn everything; I think I have beaten
>> it into submission except for one final error. If you can think of
>> something obvious for me to check I would appreciate it.
>
> Please send amber-related questions to the mail reflector,
> amber_at_scripps.edu.
> That way, many people can see your question and try to help, and
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> information on how to subscribe.
>
>> addAtomTypes {{"NL" "N" "sp2"}{"OL" "O" "sp2"}}
>
>> For atom: .R<HIC 96>.A<NE2 12> Could not find type: NL
>
> You need to create a frcmod file that defines the atom type NL (its
> mass
> and van der Waals parameters), plus any parameters for bonds it is
> a part of.
> The addAtomTypes command just gives a hybridization and tells leap
> what
> the atomic number is. You need this plus th info in the frcmod file.
>
> Tutorial 4 should give you some ideas, as it does something like
> what you
> want:
>
> http://www.rosswalker.co.uk/tutorials/amber_workshop/
> Tutorial_four/
>
> ...good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | skype: dacase
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================

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