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

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Mon Jun 18 13:29:14 CEST 2007

By the way, I just tried D-alanine with the residue name DALA. In this case, D-alanine doesn’t flip to L-alanine. So it seems that the order  CA-N-C-CB is different from CA-C-N-CB. It seems that I havent totally understand the defintion and sign of improper angle.


-----Original Message-----
From: Hu Zhongqiao 
Sent: 2007年6月18日 7:03 PM
To: 'gmx-users at gromacs.org'
Subject: RE: non-intergral charge for L-alanine molecules?

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 

 [ impropers ]
;  ai    aj    ak    al   gromos type
    CA     N     C    CB     gi_2 

 [ 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,


Mark Abraham wrote:
>> I want to simulated transport of D- and L- alanine molecules. First I 
>> tried using ffg43a1 force field, but D-analine will quickly flip to 
>> L-alanine during energy minimization (I dont know why).
> I guess either you gave it the wrong enantiomer to start with, or your 
> minimization step was too large and you happened to induce a flip with 
> one force field and not the other. There's nothing about any force 
> field that will cause preference for one enantiomer over another.
In Gromos there is: the angle for the improper dihedral.

>> Alternatively, I
>> tried oplsaa force fields. That's OK without flip from D- to L-. But 
>> one problem is that when I used
>> pdb2gmx -f L_alanine.pdb -p L_alanine.top -o L_alanine.gro -ff oplsaa
>> The produced L_alanine.top showed that L_alanine molecule has 
>> non-integral charge, which is obvioulsy unrealisitc.
>> I found that charges of atoms in L_alanine molecule are different 
>> from charges of corresponding atoms in ALA residue. I want to ask
>> (1) why L_alanine molecule has non-integral charge? Is it right?
>> (2) why identical atoms in L_alanine and ALA residue have different 
>> charges?
> Would you expect a carbon and oxygen in a mid-chain residue to have 
> the same partial charge as a carbon and oxygen in a terminal carboxyl group?
> You should read chapter five of the manual thoroughly, and in 
> particular the section about termini databases.
> Then, when you use pdb2gmx to try to create a zwitterion, choose the 
> options that allow you to make one.
> Mark
For OPLSAA you can choose special Zwitterion termini. Rerun pdb2gmx with the -ter flag.

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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