[gmx-users] Amidated C-terminal

[Shima Arasteh]

The version of GROMACS I'm using is 4.5.5.
I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl C. Is there any problem with the C36 which I use? 

[ SER ]
 [ atoms ]
    N    NH1    -0.47    0
    HN    H    0.31    1
    CA    CT1    0.07    2
    HA    HB    0.09    3
    CB    CT2    0.05    4
    HB1    HA    0.09    5
    HB2    HA    0.09    6
    OG    OH1    -0.66    7
    HG1    H    0.43    8
    C    C    0.51    9
    O    O    -0.51    10




Sincerely,
Shima


________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, January 2, 2013 10:46 PM
Subject: Re: [gmx-users] Amidated C-terminal



On 1/2/13 2:07 PM, Shima Arasteh wrote:
>
>
>   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 :
>
>     .
>     .
>     .
>     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 ?
>

The choice of CT2 is correct.  The net charge comes from an incorrect charge 
assignment to the carbonyl C (atom 372), which should be +0.55 instead of +0.51, 
which is the charge in a normal backbone peptide bond.  The aminoacids.c.tdb 
file correctly assigns this charge, so I don't know why pdb2gmx didn't produce 
it.  I tried a protein in version 4.5.5 and it worked perfectly - which version 
are you using?  If it's not 4.5.5, upgrade and try again.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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