AMBER Archive (2006)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Mar 09 2006 - 00:18:29 CST

Dear Ye,

Did u check out whether the hydrogens are bonded to N in xleap? If yes,
did u check out whether the bond parameters for that H type and N type
are defined? If they are defined, those hydrogens should not move apart
from N.

On Thu, 9 Mar 2006, Ye Mei wrote:

> Dear Amber users£¬
>
> I am working on a drug molecule which has a positively charged guanidine group. I followed the default routine to build the parameters for this drug molecule. But after md simulation, two hydrogen atoms leave the plan of heavy atoms, which seems to be the typical -NH2 structure. I know I should modify the bond parameters, but I donot know what I should do exactly. Could anybody help me?
>
> ¡¡¡¡¡¡¡¡¡¡¡¡
>
> Best regards,
>
> Ye Mei
> ymei_at_itcc.nju.edu.cn
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2006-03-09
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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