[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer
Mijiddorj B
b.mijiddorj at gmail.com
Wed Dec 4 08:34:05 CET 2019
Dear Justin,
Thank you very much for your kind response.
Best regards,
Mijiddorj
> ------------------------------
>
> Message: 6
> Date: Tue, 3 Dec 2019 10:54:48 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
> for polymer
> Message-ID: <9a3d6542-814f-695d-676c-24262f5a008a at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 12/1/19 5:43 PM, Mijiddorj B wrote:
> > Dear Justin,
> >
> > Thank you very much for your response.
> > I copied the ITP file that generated Charmm-gui. I am sorry for copied
> this
> > long residue topology. The residue contains two capping groups that
> belong
> > to first six atoms and the last six atoms. I thought that if I cut the
> > first 6 atoms, the rest is the last residue. Similarly, after cut the
> last
> > 6 atoms, the rest will show the first residue of the polymer. If I cut
> both
> > ends, I can get the internal residue of the polymer. However, the first
> > and the last 6 atoms possess + 0.002 net charges. Because of this
> > difference, my three residues assigned as the non-neutral from pdb2gmx.
> > How can I solve this problem without any QM calculations?
>
> What you appear to have defined as a "central" residue looks like it is
> several copies of the same, so you're likely seeing the effects of small
> errors in charge accumulation, which is a common problem with polymers.
> Use a small model compound (a single monomer + capping groups) or just
> rebalance the charges by shifting +0.002 from the connecting atoms of
> the central unit to the capping groups. Such a small change in charge
> shouldn't affect any of the other parameters.
>
> -Justin
>
> > [ atoms ]
> > ; nr type resnr residu atom cgnr charge mass
> > 1 NG321 1 PEI N1 1 -0.876 14.0070
> ;
> > qtot -0.876
> > 2 HGPAM2 1 PEI H1 2 0.298 1.0080
> ;
> > qtot -0.578
> > 3 HGPAM2 1 PEI H2 3 0.298 1.0080
> ;
> > qtot -0.280
> > 4 CG321 1 PEI C1 4 0.102 12.0110
> ;
> > qtot -0.178
> > 5 HGA2 1 PEI H3 5 0.090 1.0080
> ;
> > qtot -0.088
> > 6 HGA2 1 PEI H4 6 0.090 1.0080
> ;
> > qtot 0.002
> >
> > 7 CG321 1 PEI C2 7 0.091 12.0110
> ;
> > qtot 0.093
> > 8 HGA2 1 PEI H5 8 0.090 1.0080
> ;
> > qtot 0.183
> > 9 HGA2 1 PEI H6 9 0.090 1.0080
> ;
> > qtot 0.273
> > 10 NG301 1 PEI N2 10 -0.819 14.0070
> ;
> > qtot -0.546
> > 11 CG321 1 PEI C3 11 0.091 12.0110
> ;
> > qtot -0.455
> > 12 HGA2 1 PEI H7 12 0.090 1.0080
> ;
> > qtot -0.365
> > 13 HGA2 1 PEI H8 13 0.090 1.0080
> ;
> > qtot -0.275
> > 14 CG321 1 PEI C4 14 0.005 12.0110
> ;
> > qtot -0.270
> > 15 HGA2 1 PEI H9 15 0.090 1.0080
> ;
> > qtot -0.180
> > 16 HGA2 1 PEI H10 16 0.090 1.0080
> ;
> > qtot -0.090
> > 17 NG311 1 PEI N3 17 -0.666 14.0070
> ;
> > qtot -0.756
> > 18 HGPAM1 1 PEI H11 18 0.300 1.0080
> ;
> > qtot -0.456
> > 19 CG321 1 PEI C5 19 0.005 12.0110
> ;
> > qtot -0.451
> > 20 HGA2 1 PEI H12 20 0.090 1.0080
> ;
> > qtot -0.361
> > 21 HGA2 1 PEI H13 21 0.090 1.0080
> ;
> > qtot -0.271
> > 22 CG321 1 PEI C6 22 0.091 12.0110
> ;
> > qtot -0.180
> > 23 HGA2 1 PEI H14 23 0.090 1.0080
> ;
> > qtot -0.090
> > 24 HGA2 1 PEI H15 24 0.090 1.0080
> ;
> > qtot -0.000
> > 25 NG301 1 PEI N4 25 -0.817 14.0070
> ;
> > qtot -0.817
> > 26 CG321 1 PEI C7 26 0.091 12.0110
> ;
> > qtot -0.726
> > 27 HGA2 1 PEI H16 27 0.090 1.0080
> ;
> > qtot -0.636
> > 28 HGA2 1 PEI H17 28 0.090 1.0080
> ;
> > qtot -0.546
> > 29 CG321 1 PEI C8 29 0.091 12.0110
> ;
> > qtot -0.455
> > 30 HGA2 1 PEI H18 30 0.090 1.0080
> ;
> > qtot -0.365
> > 31 HGA2 1 PEI H19 31 0.090 1.0080
> ;
> > qtot -0.275
> > 32 NG301 1 PEI N5 32 -0.815 14.0070
> ;
> > qtot -1.090
> > 33 CG321 1 PEI C9 33 0.091 12.0110
> ;
> > qtot -0.999
> > 34 HGA2 1 PEI H20 34 0.090 1.0080
> ;
> > qtot -0.909
> > 35 HGA2 1 PEI H21 35 0.090 1.0080
> ;
> > qtot -0.819
> > 36 CG321 1 PEI C10 36 0.005 12.0110
> ;
> > qtot -0.814
> > 37 HGA2 1 PEI H22 37 0.090 1.0080
> ;
> > qtot -0.724
> > 38 HGA2 1 PEI H23 38 0.090 1.0080
> ;
> > qtot -0.634
> > 39 NG311 1 PEI N6 39 -0.669 14.0070
> ;
> > qtot -1.303
> > 40 HGPAM1 1 PEI H24 40 0.300 1.0080
> ;
> > qtot -1.003
> > 41 CG321 1 PEI C11 41 0.004 12.0110
> ;
> > qtot -0.999
> > 42 HGA2 1 PEI H25 42 0.090 1.0080
> ;
> > qtot -0.909
> > 43 HGA2 1 PEI H26 43 0.090 1.0080
> ;
> > qtot -0.819
> > 44 CG321 1 PEI C12 44 0.091 12.0110
> ;
> > qtot -0.728
> > 45 HGA2 1 PEI H27 45 0.090 1.0080
> ;
> > qtot -0.638
> > 46 HGA2 1 PEI H28 46 0.090 1.0080
> ;
> > qtot -0.548
> > 47 CG321 1 PEI C13 47 0.102 12.0110
> ;
> > qtot -0.446
> > 48 HGA2 1 PEI H29 48 0.090 1.0080
> ;
> > qtot -0.356
> > 49 HGA2 1 PEI H30 49 0.090 1.0080
> ;
> > qtot -0.266
> > 50 NG321 1 PEI N7 50 -0.876 14.0070
> ;
> > qtot -1.142
> > 51 HGPAM2 1 PEI H31 51 0.298 1.0080
> ;
> > qtot -0.844
> > 52 HGPAM2 1 PEI H32 52 0.298 1.0080
> ;
> > qtot -0.546
> > 53 CG321 1 PEI C14 53 0.091 12.0110
> ;
> > qtot -0.455
> > 54 HGA2 1 PEI H33 54 0.090 1.0080
> ;
> > qtot -0.365
> > 55 HGA2 1 PEI H34 55 0.090 1.0080
> ;
> > qtot -0.275
> > 56 CG321 1 PEI C15 56 0.005 12.0110
> ;
> > qtot -0.270
> > 57 HGA2 1 PEI H35 57 0.090 1.0080
> ;
> > qtot -0.180
> > 58 HGA2 1 PEI H36 58 0.090 1.0080
> ;
> > qtot -0.090
> > 59 NG311 1 PEI N8 59 -0.669 14.0070
> ;
> > qtot -0.759
> > 60 HGPAM1 1 PEI H37 60 0.300 1.0080
> ;
> > qtot -0.459
> > 61 CG321 1 PEI C16 61 0.004 12.0110
> ;
> > qtot -0.455
> > 62 HGA2 1 PEI H38 62 0.090 1.0080
> ;
> > qtot -0.365
> > 63 HGA2 1 PEI H39 63 0.090 1.0080
> ;
> > qtot -0.275
> > 64 CG321 1 PEI C17 64 0.102 12.0110
> ;
> > qtot -0.173
> > 65 HGA2 1 PEI H40 65 0.090 1.0080
> ;
> > qtot -0.083
> > 66 HGA2 1 PEI H41 66 0.090 1.0080
> ;
> > qtot 0.007
> > 67 NG321 1 PEI N9 67 -0.876 14.0070
> ;
> > qtot -0.869
> > 68 HGPAM2 1 PEI H42 68 0.298 1.0080
> ;
> > qtot -0.571
> > 69 HGPAM2 1 PEI H43 69 0.298 1.0080
> ;
> > qtot -0.273
> > 70 CG321 1 PEI C18 70 0.091 12.0110
> ;
> > qtot -0.182
> > 71 HGA2 1 PEI H44 71 0.090 1.0080
> ;
> > qtot -0.092
> > 72 HGA2 1 PEI H45 72 0.090 1.0080
> ;
> > qtot -0.002
> > 73 CG321 1 PEI C19 73 0.091 12.0110
> ;
> > qtot 0.089
> > 74 HGA2 1 PEI H46 74 0.090 1.0080
> ;
> > qtot 0.179
> > 75 HGA2 1 PEI H47 75 0.090 1.0080
> ;
> > qtot 0.269
> > 76 NG301 1 PEI N10 76 -0.817 14.0070
> ;
> > qtot -0.548
> > 77 CG321 1 PEI C20 77 0.091 12.0110
> ;
> > qtot -0.457
> > 78 HGA2 1 PEI H48 78 0.090 1.0080
> ;
> > qtot -0.367
> > 79 HGA2 1 PEI H49 79 0.090 1.0080
> ;
> > qtot -0.277
> > 80 CG321 1 PEI C21 80 0.102 12.0110
> ;
> > qtot -0.175
> > 81 HGA2 1 PEI H50 81 0.090 1.0080
> ;
> > qtot -0.085
> > 82 HGA2 1 PEI H51 82 0.090 1.0080
> ;
> > qtot 0.005
> > 83 NG321 1 PEI N11 83 -0.876 14.0070
> ;
> > qtot -0.871
> > 84 HGPAM2 1 PEI H52 84 0.298 1.0080
> ;
> > qtot -0.573
> > 85 HGPAM2 1 PEI H53 85 0.298 1.0080
> ;
> > qtot -0.275
> > 86 CG321 1 PEI C22 86 0.091 12.0110
> ;
> > qtot -0.184
> > 87 HGA2 1 PEI H54 87 0.090 1.0080
> ;
> > qtot -0.094
> > 88 HGA2 1 PEI H55 88 0.090 1.0080
> ;
> > qtot -0.004
> > 89 CG321 1 PEI C23 89 0.102 12.0110
> ;
> > qtot 0.098
> > 90 HGA2 1 PEI H56 90 0.090 1.0080
> ;
> > qtot 0.188
> > 91 HGA2 1 PEI H57 91 0.090 1.0080
> ;
> > qtot 0.278
> > 92 NG321 1 PEI N12 92 -0.876 14.0070
> ;
> > qtot -0.598
> > 93 HGPAM2 1 PEI H58 93 0.298 1.0080
> ;
> > qtot -0.300
> > 94 HGPAM2 1 PEI H59 94 0.298 1.0080
> ;
> > qtot -0.002
> >
> > 95 CG321 1 PEI C24 95 0.102 12.0110
> ;
> > qtot 0.100
> > 96 HGA2 1 PEI H60 96 0.090 1.0080
> ;
> > qtot 0.190
> > 97 HGA2 1 PEI H61 97 0.090 1.0080
> ;
> > qtot 0.280
> > 98 NG321 1 PEI N13 98 -0.876 14.0070
> ;
> > qtot -0.596
> > 99 HGPAM2 1 PEI H62 99 0.298 1.0080
> ;
> > qtot -0.298
> > 100 HGPAM2 1 PEI H63 100 0.298 1.0080
> ;
> > qtot -0.000
> >
> >
> > Best regards,
> >
> > Mijiddorj
> >
> >
> > ------------------------------
> >> Message: 6
> >> Date: Fri, 29 Nov 2019 08:21:23 -0500
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
> >> for polymer
> >> Message-ID: <883c0fb0-ee1e-e16a-215b-0a33b0a4b9c2 at vt.edu>
> >> Content-Type: text/plain; charset=utf-8; format=flowed
> >>
> >>
> >>
> >> On 11/29/19 3:27 AM, Mijiddorj B wrote:
> >>> Dear Justin,
> >>>
> >>> As you suggested, I generated the charmm36 parameter using cgenff for
> >>> single unit with two capping groups. After that, I created 3 residues
> >> based
> >>> on the parameter of cgenff including N-ter side, Middle, and C-ter side
> >>> residues. However, the net charges of these residues are not equal to
> >> zero
> >>> as -0.002, -0.004, and -0.002, respectively.
> >>>
> >>> 1. How can I adjust the charge of these residue?
> >> Your model compound surely didn't have a net -0.008 charge, so make sure
> >> you're assigning charges correctly. Without seeing your actual residue
> >> definitions, there's nothing I (or anyone else) can suggest.
> >>
> >>> 2. Is it possible to run simulation ignoring the grompp comments?
> >> When grompp tells you there's a problem, don't ignore it. If you're
> >> trying to simply override these unphysical charges, your simulation will
> >> be useless because your model does not reflect reality.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 7
> >> Date: Fri, 29 Nov 2019 08:22:15 -0500
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Calculation of RMSF
> >> Message-ID: <7d4887f6-3762-f556-fc70-ef2ea463daad at vt.edu>
> >> Content-Type: text/plain; charset=utf-8; format=flowed
> >>
> >>
> >>
> >> On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote:
> >>> Hi,
> >>>
> >>> I am confused a bit by this answer -- isn't the file specified by -s
> used
> >>> for defining the rmsf (this is what is called the "reference" structure
> >> in
> >>> the documentation, and I have found that my results do vary using a
> >>> different "-s" file)...? Or is that just used for fitting and then the
> >>> average of the resulting fitted structures is used for the rmsf?
> >>> Specifically, what is the "-s" uased for in this case?
> >> It is used for fitting. RMSF is simply the standard deviation of
> >> position, so an average structure is computed from the selected frames
> >> and the RMSF is computed from it.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> --
> >> Gromacs Users mailing list
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> >> End of gromacs.org_gmx-users Digest, Vol 187, Issue 71
> >> ******************************************************
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
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>
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