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

[David van der Spoel]

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.
>>
>> [ atoms ]
>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>> typeB    chargeB      massB
>>      1   opls_287      1    ALA      N      1       -0.3    14.0067   ;
>> qtot -0.3
>>      2   opls_290      1    ALA     H1      1       0.33      1.008   ;
>> qtot 0.03
>>      3   opls_290      1    ALA     H2      1       0.33      1.008   ;
>> qtot 0.36
>>      4   opls_290      1    ALA     H3      1       0.33      1.008   ;
>> qtot 0.69
>>      5   opls_283      1    ALA     CA      1       0.04     12.011   ;
>> qtot 0.73
>>      6   opls_140      1    ALA     HA      1       0.06      1.008   ;
>> qtot 0.79
>>      7   opls_135      1    ALA     CB      2      -0.18     12.011   ;
>> qtot 0.61
>>      8   opls_140      1    ALA    HB1      2       0.06      1.008   ;
>> qtot 0.67
>>      9   opls_140      1    ALA    HB2      2       0.06      1.008   ;
>> qtot 0.73
>>     10   opls_140      1    ALA    HB3      2       0.06      1.008   ;
>> qtot 0.79
>>     11   opls_271      1    ALA      C      3        0.7     12.011   ;
>> qtot 1.49
>>     12   opls_272      1    ALA     O1      3       -0.8    15.9994   ;
>> qtot 0.69
>>     13   opls_272      1    ALA     O2      3       -0.8    15.9994   ;
>> qtot -0.11
>>
>> I opened ffoplsaa.rtp and find the atom types for ALA residue is
>>
>> [ ALA ]
>>  [ atoms ]
>>      N    opls_238   -0.500     1
>>      H    opls_241    0.300     1
>>     CA    opls_224B   0.140     1
>>     HA    opls_140    0.060     1
>>     CB    opls_135   -0.180     2
>>    HB1    opls_140    0.060     2
>>    HB2    opls_140    0.060     2
>>    HB3    opls_140    0.060     2
>>      C    opls_235    0.500     3
>>      O    opls_236   -0.500     3
>>
>> 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.
________________________________________________________________________
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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