[gmx-users] Non integer charge value

[Justin Lemkul]

On 5/10/18 8:57 AM, Hemalatha Jayabal wrote:
> 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

What patching are you applying to the N-terminus? These charges are 
totally wrong. Make sure to apply the PRO-NH2+ patch.

-Justin

>       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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-- 
==================================================

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

==================================================