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

rose rahmani rose.rhmn93 at gmail.com
Wed Oct 31 22:20:20 CET 2018


Oh, yes. I've got t now!
Thank you so much Justin for your kind responses(as always;)).

On Thu, Nov 1, 2018 at 12:23 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/31/18 4:23 PM, rose rahmani wrote:
> >   i've tried it.But the results are exactly the same as i didn't apply
> > patches. it doesn't make any difference. So what is the purpose of using
> > -ter (COO- & NH3) when results are same in my case?
>
> I don't follow. Topology generation requires the selection of terminal
> patching of some sort, either if pdb2gmx does it for you (choosing
> defaults) or if you do it.
>
> -Justin
>
> > On Wed, 31 Oct 2018, 22:49 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 10/31/18 2:56 PM, rose rahmani wrote:
> >>> Thank you, but I couldn't understand you exactly. My structures already
> >>> have NH3+ and COO- . You mean everything is right? That's normal, yes?
> >> I was stating which terminal patches you should choose with pdb2gmx to
> >> transform the Phe .rtp topology into that of a zwitterion.
> >>
> >> -Justin
> >>
> >>> On Wed, 31 Oct 2018, 21:43 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >>>
> >>>> 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
> >>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Assistant Professor
> >>>> Virginia Tech Department of Biochemistry
> >>>>
> >>>> 303 Engel Hall
> >>>> 340 West Campus Dr.
> >>>> Blacksburg, VA 24061
> >>>>
> >>>> jalemkul at vt.edu | (540) 231-3129
> >>>> http://www.thelemkullab.com
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> posting!
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> >>>>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
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> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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