[gmx-users] Zwitterionic amino acid topology parameters in CHARMM
rose rahmani
rose.rhmn93 at gmail.com
Wed Oct 31 21:23:34 CET 2018
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?
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
>
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