normal Histidine Protonation with elnedyn22

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6 years 9 months ago #4881 by Samuel
Histidine Protonation with elnedyn22 was created by Samuel
Dear Martini Users,

I'm new to Martini and I'm trying to use martini to simulate several protein, and I notice an issue when using martinize.py with elnedyn22.

The charge is the same watever protonation I indicate to martinize :
HIH:
31 Nda 15 HIH BB 31 0.0000 ; T
32 SC4 15 HIH SC1 32 0.0000 ; T
33 SP1 15 HIH SC2 33 0.0000 ; T
34 SP1 15 HIH SC3 34 0.0000 ; T
HIS:
31 Nda 15 HIS BB 31 0.0000 ; T
32 SC4 15 HIS SC1 32 0.0000 ; T
33 SP1 15 HIS SC2 33 0.0000 ; T
34 SP1 15 HIS SC3 34 0.0000 ; T

I also notice in the FORCE FIELD PARAMETERS section of martinize, that elnedyn22 in opposition to elnedyn22p of martini22 , had the same definition of HIS and HIH (line 2261 and 2262):

'HIS': [spl("SC4 SP1 SP1"), [(0.195, None), (0.193,None), (0.295,None), (0.216,None)], [(135,100),(115, 50)]],
'HIH': [spl("SC4 SP1 SP1"), [(0.195, None), (0.193,None), (0.295,None), (0.216,None)], [(135,100),(115, 50)]],


As in martini22 for example, the description of HIH is different :
"HIS": [spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIH": [spl("SC4 SP1 SQd"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],


I guess that is a bug, and that I should correct martinize with the same value of martini22.

Cheers,
Samuel

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1 month 2 weeks ago #9389 by qiaobf
Replied by qiaobf on topic Histidine Protonation with elnedyn22
Hi Samuel,
I changed the line below in "class elnedyn22:"

#'HIH': [spl("SC4 SP1 SP1"), [(0.195, None), (0.193,None), (0.295,None), (0.216,None)], [(135,100),(115, 50)]],
'HIH': [spl("SC4 SP1 SQd"), [(0.195, None), (0.193,None), (0.295,None), (0.216,None)], [(135,100),(115, 50)]],

Best,
Baofu

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