AMBER Archive (2002)

Subject: Re: amber question

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Mon Sep 16 2002 - 12:24:20 CDT

link input residue names are 16 to a line

On Mon, 16 Sep 2002, David A. Case wrote:

>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
>
> 

-- 

----------------------------------------------------------------------------
James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue                      
University of California                  
San Francisco, CA 94143-0446               
----------------------------------------------------------------------------