[gmx-users] genion question
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 26 02:07:48 CEST 2009
Paymon Pirzadeh wrote:
> 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:
>
You chose the wrong terminus. The Zwitterion-NH3+ species is for an isolated
amino acid containing both NH3+ and COO- alpha-carbon substituents. Choose a
plain NH3+ for your terminus.
-Justin
> 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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>>
>
>
--
========================================
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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