AMBER Archive (2006)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Mar 09 2006 - 01:22:17 CST

Dear Ye,

I do not know the structural characteristics of guanidine, but even if the
-NH2 group has a planar structure it is normal to see it non-planar
during the simulation. But how much it is off from the planar structure
is important.

In order to give this -NH2 group a planar structure, u need to define the
improper torsional angles. Check out the following address, which has the
formats used in AMBER:

http://amber.scripps.edu/formats.html#frcmod

You need to create an .frcmod file in order to describe this improper
torsional angles for these H and N type atoms.

When all is set, the -NH2 group will be off from planar structure during
the simulation, but not too much. But if u minimize the structure using
this .frcmod file, u will get a planar structure for sure (if the improper
torsional angles are defined right).

The question is, how to create this .frcmod file. Check out your
$AMBERHOME/dat/leap/parm directory. You will see some frcmod files in this
directory. This might help u to create your own frcmod file.

Hope this might help. Good luck...

On Thu, 9 Mar 2006, Ye Mei wrote:

> Dear Ilyas,
>
> Thank you very much for your reply. Maybe I have not made myself clear.
> H21 H22
> \ /
> N2
> //
> -N1--C1 (+1 charge)
> | \
> H1 N3
> / \
> H31 H32
> In above guanidine group, all atoms should be in the same plane, right?
> But after md simulation, H31 and H32 leave this plane. They still bond to N3.
> I know I should modify the parameters for bonds N1-C1, C1-N2 and C1-N3. They all
> possess some properties like double-bond. But I donot know how to make it.
>
>
> ======= 2006-03-09 14:18:29 Ilyas Yildirim wrote=======
>
> >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 - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
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>
>
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡
>
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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