[gmx-users] Zwitterionic amino acid topology parameters in CHARMM
rose rahmani
rose.rhmn93 at gmail.com
Wed Oct 31 20:00:04 CET 2018
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?
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
>
> ==================================================
>
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