----- Original Message -----
From: "Ye MEI" <ymei.itcc.nju.edu.cn>
To: "amber mailing list" <amber.scripps.edu>
Sent: Tuesday, April 19, 2005 10:23 AM
Subject: AMBER: a problem with mm_pbsa
> Dear amber users,
>
> I am trying mm_pbsa to test the binding stability of a peptide/ligand
> complex. But pb calculation starting from one snapshot gives an error
> message in the output file as:
> PB bomb in pb_reslist(): maxnbr too small
> I researched the mailing list and found that cutres should be set to 12 or
> higher. But the manual of amber8 says that the default value for cutres is
> 12. And in the input file of mm_pbsa, there is no such option to modify
> the value of cutres.
> What should I do then?
>
>
>
I got the same question before. I modified the script in
amber8/src/mm_pbsa/mm_pbsa_creatinput.pm (section: sub_creat_pbsa_input) by
adding cutres =12, and it works.
Xin
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Received on Tue Apr 19 2005 - 15:53:00 PDT
