[gmx-users] Amidated C-terminal

[Shima Arasteh]

 Hi,

In order to make an amidated c-terminal, I used CT2 in charmm ff at the c-terminal. The last residue of my peptide is serine, and the total charge of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the c-terminal, and then getting top file, when I see the top file, everything is ok up to the amidated serine residue. But something wrong is with the charged amidated serine; the total charge is not equal to 5.00 :

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   361          C     22    LYS      C    361       0.51     12.011   ; qtot 5.51
   362          O     22    LYS      O    362      -0.51     15.999   ; qtot 5
; residue  23 SER rtp SER  q -0.0
   363        NH1     23    SER      N    363      -0.47     14.007   ; qtot 4.53
   364          H     23    SER     HN    364       0.31      1.008   ; qtot 4.84
   365        CT1     23    SER     CA    365       0.07     12.011   ; qtot 4.91
   366         HB     23    SER     HA    366       0.09      1.008   ; qtot 5
   367        CT2     23    SER     CB    367       0.05     12.011   ; qtot 5.05
   368         HA     23    SER    HB1    368       0.09      1.008   ; qtot 5.14
   369         HA     23    SER    HB2    369       0.09      1.008   ; qtot 5.23
   370        OH1     23    SER     OG    370      -0.66     15.999   ; qtot 4.57
   371          H     23    SER    HG1    371       0.43      1.008   ; qtot 5
   372          C     23    SER      C    372       0.51     12.011   ; qtot 5.51
   373        NH2     23    SER     NT    373      -0.62     14.007   ; qtot 4.89
   374          H     23    SER    HT1    374        0.3      1.008   ; qtot 5.19
   375          H     23    SER    HT2    375       0.32      1.008   ; qtot 5.51
   376          O     23    SER      O    376      -0.55     15.999   ; qtot 4.96

I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last residue is positive charged? Do the defined atom charges are supposed to be modified in last residue ?

Would you please give me suggestions?
Thanks in advance.
 


Sincerely,
Shima