[gmx-users] genion question
Paymon Pirzadeh
ppirzade at ucalgary.ca
Wed Aug 26 02:06:12 CEST 2009
Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:
1 opls_287 1 ASP N 1 -0.3 14.0067 ; qtot
-0.3
2 opls_290 1 ASP H1 1 0.33 1.008 ;
qtot 0.03
3 opls_290 1 ASP H2 1 0.33 1.008 ;
qtot 0.36
4 opls_290 1 ASP H3 1 0.33 1.008 ;
qtot 0.69
5 opls_299 1 ASP CA 1 0.15 12.011 ;
qtot 0.84
6 opls_140 1 ASP HA 1 0.06 1.008 ;
qtot 0.9
7 opls_274 1 ASP CB 2 -0.22 12.011 ;
qtot 0.68
8 opls_140 1 ASP HB1 2 0.06 1.008 ;
qtot 0.74
9 opls_140 1 ASP HB2 2 0.06 1.008 ;
qtot 0.8
10 opls_271 1 ASP CG 3 0.7 12.011 ;
qtot 1.5
11 opls_272 1 ASP OD1 3 -0.8 15.9994 ;
qtot 0.7
12 opls_272 1 ASP OD2 3 -0.8 15.9994 ;
qtot -0.1
13 opls_235 1 ASP C 4 0.5 12.011 ;
qtot 0.4
14 opls_236 1 ASP O 4 -0.5 15.9994 ;
qtot -0.1
What do you think?
Payman
On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote:
>
> Paymon Pirzadeh wrote:
> > Well, when I look into my .top file, almost no where I see closeness to
> > an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
> > sometimes. But I can not see a clear trend on where things go wrong. My
> > protein has only 37 amino acids with 451 atoms (including hydrogens).
> > I am not sure if I can attach the .top file to my e-mail for you to
> > check. This way I could learn where and how things go wrong!
> >
>
> The total charge will undoubtedly fluctuate. What's most important to look at
> is when you reach the end of a residue and you do not see an integer charge.
>
> -Justin
>
> > Payman
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Thanks for the tips!
> >>> But I still have problem with my added ion. Justin had told me that ion
> >>> names are force-field specific! Since I am using OPLSaa, I checked the
> >>> itp file for Na ion name, and it was Na+. I used this name with the
> >> No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section:
> >>
> >> [ moleculetype ]
> >> ; molname nrexcl
> >> NA+ 1
> >>
> >> [ atoms ]
> >> ; id at type res nr residu name at name cg nr charge mass
> >> 1 opls_407 1 NA+ NA 1 1 22.98977
> >>
> >>> -pname switch, but again during the grompp I ran into the following
> >>> error:
> >>> Warning: atom name 65870 in AFP_I.top and
> >>> AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
> >>>
> >>> WARNING 1 [file AFP_I.top, line 4151]:
> >>> 1 non-matching atom name
> >>> atom names from AFP_I.top will be used
> >>> atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
> >>>
> >>> I really do not know what I am doing wrong here! Also regarding past
> >>> discussions, adding this single ion has lead into the following note:
> >>>
> >>> NOTE 1 [file AFP_I.top, line 4151]:
> >>> System has non-zero total charge: 1.000000e-02
> >>>
> >>> I am not sure if that much charge will cause me troubles or not!
> >>>
> >> I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top
> >> to see where things start going wrong (i.e., not an integer). I would think
> >> your system would have to be quite large to accumulate such a difference in charge.
> >>
> >> -Justin
> >>
> >>> Payman
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> >>>> Paymon Pirzadeh wrote:
> >>>>> Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> >>>>> negative charge exactly? Does that hurt science or simulation?
> >>>> It's probably irrelevant. The representation of "decimal" numbers on
> >>>> computers can be inexact, such that things like 0.02 added to itself 100
> >>>> times does not pass a test for equality with 2. You may be observing
> >>>> this kind of thing here. Your protein's [atoms] directive has a running
> >>>> count of the total charge on the molecule - go and read it and see that
> >>>> each residue has an integral charge. Hopefully you can observe where the
> >>>> rounding error might be occurring and you can make a judgement about
> >>>> whether this might be true.
> >>>>
> >>>> Mark
> >>>> _______________________________________________
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> >>>>
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> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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