[gmx-users] Non integer charge value

Hemalatha Jayabal hemalathajayabal at gmail.com
Fri May 11 12:21:07 CEST 2018


I apologize for the previous formatting.

[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21
12.011 ; qtot 0.9 6 HB 202 HYP HA 6 0.1 1.008 ; qtot 1 7 C 202 HYP C 7 0.51
12.011 ; qtot 1.51 8 O 202 HYP O 8 -0.51 15.999 ; qtot 1 9 CP2 202 HYP CB 9
-0.18 12.011 ; qtot 0.82 10 HA 202 HYP HB1 10 0.09 1.008 ; qtot 0.91 11 HA
202 HYP HB2 11 0.09 1.008 ; qtot 1 12 CP2 202 HYP CG 12 0.14 12.011 ; qtot
1.14 13 HA 202 HYP HG 13 0.09 1.008 ; qtot 1.23 14 CP3 202 HYP CD 14 0
12.011 ; qtot 1.23 15 HA 202 HYP HD21 15 0.09 1.008 ; qtot 1.32 16 HA 202
HYP HD22 16 0.09 1.008 ; qtot 1.41 17 OH1 202 HYP OD1 17 -0.66 15.999 ;
qtot 0.75 18 H 202 HYP HD1 18 0.43 1.008 ; qtot 1.18 Sequence (From PDB
file) SEQRES 1 A 7 GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 7 HYP GLY PRO HYP
GLY PRO HYP SEQRES 1 C 7 PRO HYP GLY PRO HYP GLY PRO The below is the
topology where the residue is not present as termini ; residue 205 HYP rtp
HYP q 0.0 40 N 205 HYP N 40 -0.29 14.007 ; qtot 0.89 41 CP1 205 HYP CA 41
0.02 12.011 ; qtot 0.91 42 HB 205 HYP HA 42 0.09 1.008 ; qtot 1 43 C 205
HYP C 43 0.51 12.011 ; qtot 1.51 44 O 205 HYP O 44 -0.51 15.999 ; qtot 1 45
CP2 205 HYP CB 45 -0.18 12.011 ; qtot 0.82 46 HA 205 HYP HB1 46 0.09 1.008
; qtot 0.91 47 HA 205 HYP HB2 47 0.09 1.008 ; qtot 1 48 CP2 205 HYP CG 48
0.14 12.011 ; qtot 1.14 49 HA 205 HYP HG 49 0.09 1.008 ; qtot 1.23 50 CP3
205 HYP CD 50 0 12.011 ; qtot 1.23 51 HA 205 HYP HD21 51 0.09 1.008 ; qtot
1.32 52 HA 205 HYP HD22 52 0.09 1.008 ; qtot 1.41 53 OH1 205 HYP OD1 53
-0.66 15.999 ; qtot 0.75 54 H 205 HYP HD1 54 0.43 1.008 ; qtot 1.18

On 11-May-2018 12:06, "Hemalatha Jayabal" <hemalathajayabal at gmail.com>
wrote:

I applied the said terminus as well but I ended up getting the same error.


[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21
12.011 ; qtot 0.9 6 HB 202 HYP HA 6 0.1 1.008 ; qtot 1 7 C 202 HYP C 7 0.51
12.011 ; qtot 1.51 8 O 202 HYP O 8 -0.51 15.999 ; qtot 1 9 CP2 202 HYP CB 9
-0.18 12.011 ; qtot 0.82 10 HA 202 HYP HB1 10 0.09 1.008 ; qtot 0.91 11 HA
202 HYP HB2 11 0.09 1.008 ; qtot 1 12 CP2 202 HYP CG 12 0.14 12.011 ; qtot
1.14 13 HA 202 HYP HG 13 0.09 1.008 ; qtot 1.23 14 CP3 202 HYP CD 14 0
12.011 ; qtot 1.23 15 HA 202 HYP HD21 15 0.09 1.008 ; qtot 1.32 16 HA 202
HYP HD22 16 0.09 1.008 ; qtot 1.41 17 OH1 202 HYP OD1 17 -0.66 15.999 ;
qtot 0.75 18 H 202 HYP HD1 18 0.43 1.008 ; qtot 1.18 Sequence (From PDB
file) SEQRES 1 A 7 GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 7 HYP GLY PRO HYP
GLY PRO HYP SEQRES 1 C 7 PRO HYP GLY PRO HYP GLY PRO The below is the
topology where the residue is not present as termini ; residue 205 HYP rtp
HYP q 0.0 40 N 205 HYP N 40 -0.29 14.007 ; qtot 0.89 41 CP1 205 HYP CA 41
0.02 12.011 ; qtot 0.91 42 HB 205 HYP HA 42 0.09 1.008 ; qtot 1 43 C 205
HYP C 43 0.51 12.011 ; qtot 1.51 44 O 205 HYP O 44 -0.51 15.999 ; qtot 1 45
CP2 205 HYP CB 45 -0.18 12.011 ; qtot 0.82 46 HA 205 HYP HB1 46 0.09 1.008
; qtot 0.91 47 HA 205 HYP HB2 47 0.09 1.008 ; qtot 1 48 CP2 205 HYP CG 48
0.14 12.011 ; qtot 1.14 49 HA 205 HYP HG 49 0.09 1.008 ; qtot 1.23 50 CP3
205 HYP CD 50 0 12.011 ; qtot 1.23 51 HA 205 HYP HD21 51 0.09 1.008 ; qtot
1.32 52 HA 205 HYP HD22 52 0.09 1.008 ; qtot 1.41 53 OH1 205 HYP OD1 53
-0.66 15.999 ; qtot 0.75 54 H 205 HYP HD1 54 0.43 1.008 ; qtot 1.18


  Thank you!



On Fri 11 May, 2018, 00:11 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 5/10/18 8:57 AM, Hemalatha Jayabal wrote:
> > The magnitude of the charge is 0.18 and I hope such magnitude cannot be
> > ignored. Please find the topology of the protein chain(specific residue)
> in
> > which the error is occuring
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB
> >    chargeB      massB
> > ; residue 202 HYP rtp HYP  q +0.2
> >       1        NH2    202    HYP      N      1      -0.96     14.007   ;
> > qtot -0.96
> >       2          H    202    HYP    HT1      2       0.34      1.008   ;
> > qtot -0.62
> >       3          H    202    HYP    HT2      3       0.34      1.008   ;
> > qtot -0.28
>
> What patching are you applying to the N-terminus? These charges are
> totally wrong. Make sure to apply the PRO-NH2+ patch.
>
> -Justin
>
> >       4        CT1    202    HYP     CA      4       0.19     12.011   ;
> > qtot -0.09
> >       5         HB    202    HYP     HA      5       0.09      1.008   ;
> > qtot 0
> >       6          C    202    HYP      C      6       0.51     12.011   ;
> > qtot 0.51
> >       7          O    202    HYP      O      7      -0.51     15.999   ;
> > qtot 0
> >       8        CP2    202    HYP     CB      8      -0.18     12.011   ;
> > qtot -0.18
> >       9         HA    202    HYP    HB1      9       0.09      1.008   ;
> > qtot -0.09
> >      10         HA    202    HYP    HB2     10       0.09      1.008   ;
> > qtot 0
> >      11        CP2    202    HYP     CG     11       0.14     12.011   ;
> > qtot 0.14
> >      12         HA    202    HYP     HG     12       0.09      1.008   ;
> > qtot 0.23
> >      13        CP3    202    HYP     CD     13          0     12.011   ;
> > qtot 0.23
> >      14         HA    202    HYP   HD21     14       0.09      1.008   ;
> > qtot 0.32
> >      15         HA    202    HYP   HD22     15       0.09      1.008   ;
> > qtot 0.41
> >      16        OH1    202    HYP    OD1     16      -0.66     15.999   ;
> > qtot -0.25
> >      17          H    202    HYP    HD1     17       0.43      1.008   ;
> > qtot 0.18
> >
> >
> >
> > On Thu 10 May, 2018, 18:07 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:
> >>> Hi all,
> >>>
> >>> I have added a non standard amino acid 'Hydroxyproline' to my
> forcefield
> >>> (from literature) Charmm27 and after using pdb2gmx i could see that the
> >>> system has a non integer charge value for 1 protein chain out of 3
> >> protein
> >>> chains.  (All 3 chains contain the non standard amino acid)
> >>>    The problem is occuring in the chain in which the terminal residue
> is
> >> this
> >>> hydroxyproline. (All other places where the 'HYP' residue appears, the
> >>> charge is 0). I tried using different terminii just to be sure that the
> >>> problem is not because of the terminii.
> >>>
> >>> What should be done in such a case?
> >> That depends on if the magnitude of the charge is meaningful or not. If
> >> you have two "correct" chains and one "incorrect" chain, that suggests
> >> that nothing is likely wrong with your HYP residue so things should be
> >> fine, but refer to
> >> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic to be
> >> sure. The current version of GROMACS (2018.1) handles these rounding
> >> issues better to trigger fewer false warnings.
> >>
> >> -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
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> 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
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list