[gmx-users] RE: non-intergral charge for L-alanine molecules?

[David van der Spoel]

Hu Zhongqiao wrote:
> Thanks a lot, Mark Abraham and David,
> 
> I thought the atom charge of an ALA molecule was same as those in ALA
> residue of a protein molecules. That's wrong.
> 
> Now I can use pdb2gmx -ter to set zwitterion-type ALA.
> 
> About ffG43a1, I want to ask a question which is a little ambiguous to
> me.
> According to what someone said in mailing list, the force fields of
> D-amino acids and L-amino acids are same. One just needs set different
> coordinates for them and use the same force field. In fact I am not sure
> for this. But when I used the ALA residue name for both D- and L-
> alanine .pdb files and do energy minimization, the D-alanine quickly
> flip to L-alanine. So it seems I am missing something.
>  
> I check ffG43a1.rtp and only difference for ALA and DALA is 
> 
> ALA
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>     CA     N     C    CB     gi_2 
> 
> DALA
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>    CA     C     N    CB     gi_2 
> 
> I don't know what is the real difference for the order CA-N-C-CB and
> CA-C-N-CB. It is said that the improper angle is the angle between i, j,
> k and j, k, l. So I think the order CA-N-C-CB and CA-C-N-CB makes no
> difference, right? I hope I am not right so that I can change something
> to make sure that D-alanine does not flip to L-alanine. Anyone can give
> a somehow detailed clarification for this,
> 
> 
> Zhongqiao
> 
look up the gi_2 definition, and make a dgi_2 definition with the angle 
negative. ffGxxxbon.itp

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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