[gmx-users] Non integer charge value

[Hemalatha Jayabal]

The magnitude of the charge is 0.18 and I hope such magnitude cannot be
ignored. Please find the topology of the protein chain(specific residue) in
which the error is occuring
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
  chargeB      massB
; residue 202 HYP rtp HYP  q +0.2
     1        NH2    202    HYP      N      1      -0.96     14.007   ;
qtot -0.96
     2          H    202    HYP    HT1      2       0.34      1.008   ;
qtot -0.62
     3          H    202    HYP    HT2      3       0.34      1.008   ;
qtot -0.28
     4        CT1    202    HYP     CA      4       0.19     12.011   ;
qtot -0.09
     5         HB    202    HYP     HA      5       0.09      1.008   ;
qtot 0
     6          C    202    HYP      C      6       0.51     12.011   ;
qtot 0.51
     7          O    202    HYP      O      7      -0.51     15.999   ;
qtot 0
     8        CP2    202    HYP     CB      8      -0.18     12.011   ;
qtot -0.18
     9         HA    202    HYP    HB1      9       0.09      1.008   ;
qtot -0.09
    10         HA    202    HYP    HB2     10       0.09      1.008   ;
qtot 0
    11        CP2    202    HYP     CG     11       0.14     12.011   ;
qtot 0.14
    12         HA    202    HYP     HG     12       0.09      1.008   ;
qtot 0.23
    13        CP3    202    HYP     CD     13          0     12.011   ;
qtot 0.23
    14         HA    202    HYP   HD21     14       0.09      1.008   ;
qtot 0.32
    15         HA    202    HYP   HD22     15       0.09      1.008   ;
qtot 0.41
    16        OH1    202    HYP    OD1     16      -0.66     15.999   ;
qtot -0.25
    17          H    202    HYP    HD1     17       0.43      1.008   ;
qtot 0.18



On Thu 10 May, 2018, 18:07 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:
> > Hi all,
> >
> > I have added a non standard amino acid 'Hydroxyproline' to my forcefield
> > (from literature) Charmm27 and after using pdb2gmx i could see that the
> > system has a non integer charge value for 1 protein chain out of 3
> protein
> > chains.  (All 3 chains contain the non standard amino acid)
> >   The problem is occuring in the chain in which the terminal residue is
> this
> > hydroxyproline. (All other places where the 'HYP' residue appears, the
> > charge is 0). I tried using different terminii just to be sure that the
> > problem is not because of the terminii.
> >
> > What should be done in such a case?
>
> That depends on if the magnitude of the charge is meaningful or not. If
> you have two "correct" chains and one "incorrect" chain, that suggests
> that nothing is likely wrong with your HYP residue so things should be
> fine, but refer to
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic to be
> sure. The current version of GROMACS (2018.1) handles these rounding
> issues better to trigger fewer false warnings.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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