AMBER Archive (2002)

Subject: Re: amber question

From: David A. Case (case_at_scripps.edu)
Date: Mon Sep 16 2002 - 11:47:03 CDT

On Mon, Sep 16, 2002, yao yong wrote:
>
> I am writing this letter to to ask you a question of
> the using of amber5. Since I am using the precedure of
> creating link, edit and parm files, I meet a
> difficulty in writing the sequence in the link.in
> file. The first residue of the protein begins with a
> negative number
> Thr Glu Phe Lys Ala Ser ...
> -5 -4 -3 -2 -1 1 ...

Amber always numbers sequences from 1 to the number of residues. Any
translation back to other numbering schemes is up to the user.

>
> I wrote it as follws:
>
> ...
> P 1 0 1 3 1
> THR GLU PHE LYS ALA
> GLY 2SER ALA LYS LYS
> ...
>
> but it failed

As I have said a lot, just saying "it failed" is not very helpful. What
was the exact error message or symptom? If I remember this old Amber stuff,
you need to have more than 5 residues on a line for link input. Try putting
all of the residue names on a single line.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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