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
>
>
--
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Received on Mon Sep 16 2002 - 10:24:20 PDT
