[gmx-users] non-integer total charge of a Lysine molecule??
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 26 22:02:53 CEST 2008
-------- Original Message --------
Subject: Re: [gmx-users] non-integer total charge of a Lysine molecule??
Date: Thu, 26 Jun 2008 16:01:02 -0400
From: Justin A. Lemkul <jalemkul at vt.edu>
Reply-To: jalemkul at vt.edu
Organization: Virginia Tech
To: Sung Hyun Park <parksh at northwestern.edu>
References: <20080626195036.57D9235C5B at casbah.it.northwestern.edu>
>
> Now may I ask one more question?
> I was also doing the same simulation with a "neutral" Lysine, with the molecular formula
> (NH2)CH(COO-)(CH2)4NH3+, and was having a similar problem of non-integral total charge. Following
> the advice above, I repeated pdb2gmx for the neutral Lysine, this time by choosing NH2 for
> N-terminus and Zwitterion-COO- as C-terminus. Strangely it didn't solve the total charge
> problem
>
Well, you don't have a zwitterion...with respect to the backbone
elements, for which I believe the zwitterionic termini were designed.
> this time, and the total charge is still non-integer at 0.13, instead of the correct value at
> zero.(shown below)
>
And, on top of that, if you use NH2 and COO- (not the zwitterion
option), the charge ends up at 0.020! I suspect parameters were not
directly developed for this protonation state of lysine (someone please
correct me if I'm wrong).
An idea to try would be to apply the parameters of the normal COO- group
to your structure. That is, since the charge group for the carboxylate
is contained completely within these atoms, you could use pdb2gmx to
generate a neutral backbone (NH2/COOH, lysine +1 net charge), then
replace the COOH entries with the parameters for COO-, if that makes sense.
That is an incredibly ad hoc solution, and I don't know if it would work
or would even be valid. I would check the literature to see if anyone
has ever done anything related to isolated "neutral" lysine, and
definitely refer to the original OPLS papers to see how things were
parameterized.
-Justin
> What am I still doing wrong here?
> My command line and options chosen are as following (Lys.pdb is the input pdb file):
>
> -----------------------------------------------------------------------------------------
>
>> pdb2gmx -f Lys.pdb -ter -n -p
>>
> Select N-terminus type (start)
> 0: NH3+
> 1: ZWITTERION_NH3+
> 2: NH2
> 3: None
>
>> 2
>>
> N-terminus: NH2
> Select C-terminus type (end)
> 0: COO-
> 1: ZWITTERION_COO-
> 2: COOH
> 3: None
>
>> 1
>>
> C-terminus: ZWITTERION_COO-
> -----------------------------------------------------------------------------------------
>
> <first part of topol.top>
>
> #include "ffoplsaa.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 opls_900 1 LYSH N 1 -0.9 14.0067 ; qtot -0.9
> 2 opls_909 1 LYSH H1 1 0.36 1.008 ; qtot -0.54
> 3 opls_909 1 LYSH H2 1 0.36 1.008 ; qtot -0.18
> 4 opls_299 1 LYSH CA 1 0.15 12.011 ; qtot -0.03
> 5 opls_140 1 LYSH HA 1 0.06 1.008 ; qtot 0.03
> 6 opls_136 1 LYSH CB 2 -0.12 12.011 ; qtot -0.09
> 7 opls_140 1 LYSH HB1 2 0.06 1.008 ; qtot -0.03
> 8 opls_140 1 LYSH HB2 2 0.06 1.008 ; qtot 0.03
> 9 opls_136 1 LYSH CG 3 -0.12 12.011 ; qtot -0.09
> 10 opls_140 1 LYSH HG1 3 0.06 1.008 ; qtot -0.03
> 11 opls_140 1 LYSH HG2 3 0.06 1.008 ; qtot 0.03
> 12 opls_136 1 LYSH CD 4 -0.12 12.011 ; qtot -0.09
> 13 opls_140 1 LYSH HD1 4 0.06 1.008 ; qtot -0.03
> 14 opls_140 1 LYSH HD2 4 0.06 1.008 ; qtot 0.03
> 15 opls_292 1 LYSH CE 5 0.19 12.011 ; qtot 0.22
> 16 opls_140 1 LYSH HE1 5 0.06 1.008 ; qtot 0.28
> 17 opls_140 1 LYSH HE2 5 0.06 1.008 ; qtot 0.34
> 18 opls_287 1 LYSH NZ 6 -0.3 14.0067 ; qtot 0.04
> 19 opls_290 1 LYSH HZ1 6 0.33 1.008 ; qtot 0.37
> 20 opls_290 1 LYSH HZ2 6 0.33 1.008 ; qtot 0.7
> 21 opls_290 1 LYSH HZ3 6 0.33 1.008 ; qtot 1.03
> 22 opls_271 1 LYSH C 7 0.7 12.011 ; qtot 1.73
> 23 opls_272 1 LYSH O1 7 -0.8 15.9994 ; qtot 0.93
> 24 opls_272 1 LYSH O2 7 -0.8 15.9994 ; qtot 0.13
> ---------------------------------------------------------------------------------------------------
>
> Sorry for many questions and many thanks in advance for your kind help!
>
> Regards,
> Sung Hyun
>
>
>
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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