Fw: [gmx-users] Amidated C-terminal

[Shima Arasteh]

Have a look at CT2 in aminoacids.c.tdb please:

[ CT2 ]
[ replace ]
 O        CC        12.011    0.55
 O        O        15.9994    -0.55


It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file have +0.51 charge.
I think the amidated C-terminal in my top file should be charged +0.55 as what I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 charge for this last residue?

 
Sincerely,
Shima


----- Original Message -----
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>
Cc: 
Sent: Thursday, January 3, 2013 2:24 PM
Subject: Re: Fw: [gmx-users] Amidated C-terminal



On 1/3/13 1:00 AM, Shima Arasteh wrote:
>
>
>
>
>
>
> 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?
>

Probably.  Check the aminoacids.c.tdb file as well, it may not be correct.  I 
used the standard charmm27.ff for my test and it worked fine.

-Justin

> [ 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

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