[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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> >>>>
> >> --
> >> ==================================================
> >>
> >> 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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