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