[gmx-users] Zwitterionic amino acid topology parameters in CHARMM

[Justin Lemkul]

On 10/31/18 2:01 PM, rose rahmani wrote:
> Hi,
>
> I want to use zwitterionic form of AAs in CHARMM ff. I gave structure in
> Discovery studio and then use pdb2gmx to get its topology and ... files.
> But the number of atoms in topol.top and also some atom's partial charges
> are different from atoms and charges in aminoacids.rtp
> For example, in the case of phenylalanine,
> this is topology file after pdb2gmx:
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>    chargeB      massB
> ; residue   1 PHE rtp PHE  q  0.0
>       1        NH3      1    PHE      N      1       -0.3     14.007   ;
> qtot -0.3
>       2         HC      1    PHE     H1      2       0.33      1.008   ;
> qtot 0.03
>       3         HC      1    PHE     H2      3       0.33      1.008   ;
> qtot 0.36
>       4         HC      1    PHE     H3      4       0.33      1.008   ;
> qtot 0.69
>       5        CT1      1    PHE     CA      5       0.21     12.011   ;
> qtot 0.9
>       6         HB      1    PHE     HA      6        0.1      1.008   ;
> qtot 1
>       7        CT2      1    PHE     CB      7      -0.18     12.011   ;
> qtot 0.82
>       8         HA      1    PHE    HB1      8       0.09      1.008   ;
> qtot 0.91
>       9         HA      1    PHE    HB2      9       0.09      1.008   ;
> qtot 1
>      10         CA      1    PHE     CG     10          0     12.011   ;
> qtot 1
>      11         CA      1    PHE    CD1     11     -0.115     12.011   ;
> qtot 0.885
>      12         HP      1    PHE    HD1     12      0.115      1.008   ;
> qtot 1
>      13         CA      1    PHE    CE1     13     -0.115     12.011   ;
> qtot 0.885
>      14         HP      1    PHE    HE1     14      0.115      1.008   ;
> qtot 1
>      15         CA      1    PHE     CZ     15     -0.115     12.011   ;
> qtot 0.885
>      16         HP      1    PHE     HZ     16      0.115      1.008   ;
> qtot 1
>      17         CA      1    PHE    CD2     17     -0.115     12.011   ;
> qtot 0.885
>      18         HP      1    PHE    HD2     18      0.115      1.008   ;
> qtot 1
>      19         CA      1    PHE    CE2     19     -0.115     12.011   ;
> qtot 0.885
>      20         HP      1    PHE    HE2     20      0.115      1.008   ;
> qtot 1
>      21         CC      1    PHE      C     21       0.34     12.011   ;
> qtot 1.34
>      22         OC      1    PHE    OT1     22      -0.67     15.999   ;
> qtot 0.67
>      23         OC      1    PHE    OT2     23      -0.67     15.999   ;
> qtot 0
>
> and this is .rtp file for PHE:
>
> [ PHE ]
>   [ atoms ]
>          N       NH1     -0.47   0
>          HN      H       0.31    1
>          CA      CT1     0.07    2
>          HA      HB      0.09    3
>          CB      CT2     -0.18   4
>          HB1     HA      0.09    5
>          HB2     HA      0.09    6
>          CG      CA      0.00    7
>          CD1     CA      -0.115  8
>          HD1     HP      0.115   9
>          CE1     CA      -0.115  10
>          HE1     HP      0.115   11
>          CZ      CA      -0.115  12
>          HZ      HP      0.115   13
>          CD2     CA      -0.115  14
>          HD2     HP      0.115   15
>          CE2     CA      -0.115  16
>          HE2     HP      0.115   17
>          C       C       0.51    18
>          O       O       -0.51   19
> so as you see there O and 2 H more...  . I know that's because of COO group
> and HH.. but which of them are the real structure of zwitterionic form of
>   amino acid in force field? are both true? I would be appreciated if you
> can help me.

Just apply the normal NH3+ and COO- terminal patches. There are no 
special zwitterion patches like in some force fields (OPLS, etc.) 
Naturally, the .rtp will change - that is the function of the .tdb entries.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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