[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer
Justin Lemkul
jalemkul at vt.edu
Tue Dec 3 16:55:02 CET 2019
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
>>
>> ==================================================
>>
>>
>>
>> ------------------------------
>>
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--
==================================================
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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