AMBER Archive (2006)

Subject: Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group

From: Ye Mei (
Date: Sat Mar 11 2006 - 11:01:53 CST

Hi, Bill,

Thank you for your help. But I still have problem with it. I checked the types of these atoms. All N atoms are of nh type, and C1 are of c2 type. So I think they should be in a plane. But after minimization of the whole protein, H21 and H22 rotate along C1-N2 bond. I guess this should not happen.
Can you help me to solve it?

       H21 H22
        \ /
 C2 N2
  \ //
   N1--C1 (+1 charge)
  / \
 C3 N3
        / \
       H31 H32

Best regards,
Ye Mei
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

======= 2006-03-10 03:24:57 Bill Ross wrote=======

>Adding improper torsions to a prepin file will do *nothing* since
>they are ignored by leap. You need to make sure that the atom
>types of you NH2 and the C match an improper in the parameters.
>The simple way is to look at the types in an NH2 group in an
>existing residue and think about whether your types are correct
>or whether you need to add an improper to your parameters. If you
>do, best to make sure that it isn't picked up in another place
>that you don't want it. If you load a prepin with an IMPROPER
>section, leap will remember (but not use) them and will show
>them on saveamberparm in a helpful way.
>The AMBER Mail Reflector
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