[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer
Mijiddorj B
b.mijiddorj at gmail.com
Sun Dec 1 23:44:05 CET 2019
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?
[ 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
>
> ==================================================
>
>
>
> ------------------------------
>
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