[gmx-users] Simulation of Primed DNA-rtp entry and Terminal residue
Singh
raghavbioinfo at gmail.com
Wed Jul 6 15:25:47 CEST 2011
Hi Justin,
Thanks for quick response :)
Basically I don't want terminal H atom.. instead of that I want O+ at 3' end and -CH2-O-PO3 at second. but it is appearing on both the ends... :(
Any suggestions?
Raghav
Research Scholar
IEMN, University of Science and Technology
Villeneuve d'ascq, Lille, France
On 6 juil. 2011, at 15:08, gmx-users-request at gromacs.org wrote:
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> 1. Re: Register (Rossen Apostolov)
> 2. Re: make a new bond in VERSION 4.5.4 (Justin A. Lemkul)
> 3. Re: Questions about GB parameters (Justin A. Lemkul)
> 4. Re: Simulation of Primed DNA (Singh)
> 5. Re: Simulation of Primed DNA (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 06 Jul 2011 13:35:40 +0300
> From: Rossen Apostolov <rossen at kth.se>
> Subject: Re: [gmx-users] Register
> To: Saeid Akbarshahi <saeidakbarshahi at yahoo.com>, Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E143A7C.20408 at kth.se>
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> Rossen
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 06 Jul 2011 07:00:11 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] make a new bond in VERSION 4.5.4
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E14403B.1020902 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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>
>
> Yulian Gavrilov wrote:
>> Dear Justin, gmx users,
>>
>> I forgot to write, but I added these new residues to aminoacids.rtp.
>>
>> Maybe I need to add them also to aminoacids.r2b? How to do it correctly?
>
> An .r2b entry is unnecessary in this case; these files are only used to
> standardize force field-specific names for certain residues.
>
>> Just new lines in it or add them to lines of Gly and Lys? So, I suppose
>> it is all steps in
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>
>
> These should be all the necessary steps.
>
> -Justin
>
>>
>> [ LYQ ]
>>
>> [ atoms ]
>>
>> N N -0.41570 1
>>
>> H H 0.27190 2
>>
>> CA CT -0.07206 3
>>
>> HA H1 0.09940 4
>>
>> CB CT -0.04845 5
>>
>> HB1 HC 0.03400 6
>>
>> HB2 HC 0.03400 7
>>
>> CG CT 0.06612 8
>>
>> HG1 HC 0.01041 9
>>
>> HG2 HC 0.01041 10
>>
>> CD CT -0.03768 11
>>
>> HD1 HC 0.01155 12
>>
>> HD2 HC 0.01155 13
>>
>> CE CT 0.32604 14
>>
>> HE1 HP -0.03358 15
>>
>> HE2 HP -0.03358 16
>>
>> NZ N -0.64977 17
>>
>> HZ1 H 0.38604 18
>>
>> C C 0.59730 19
>>
>> O O -0.56790 20
>>
>> [ bonds ]
>>
>> N H
>>
>> N CA
>>
>> CA HA
>>
>> CA CB
>>
>> CA C
>>
>> CB HB1
>>
>> CB HB2
>>
>> CB CG
>>
>> CG HG1
>>
>> CG HG2
>>
>> CG CD
>>
>> CD HD1
>>
>> CD HD2
>>
>> CD CE
>>
>> CE HE1
>>
>> CE HE2
>>
>> CE NZ
>>
>> NZ HZ1
>>
>> C O
>>
>> -C N
>>
>> [ impropers ]
>>
>> -C CA N H
>>
>> CA +N C O
>>
>>
>>
>> [ GLQ ]
>>
>> [ atoms ]
>>
>> N N -0.41570 1
>>
>> H H 0.27190 2
>>
>> CA CT -0.02520 3
>>
>> HA1 H1 0.06980 4
>>
>> HA2 H1 0.06980 5
>>
>> C C 0.59730 6
>>
>> O O -0.56790 7
>>
>> [ bonds ]
>>
>> N H
>>
>> N CA
>>
>> CA HA1
>>
>> CA HA2
>>
>> CA C
>>
>> C O
>>
>> -C N
>>
>> [ impropers ]
>>
>> -C CA N H
>>
>> CA +N C O
>>
>>
>> --
>>
>> Sincerely,
>>
>> Yulian Gavrilov
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 06 Jul 2011 08:02:09 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Questions about GB parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E144EC1.1060008 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Per Larsson wrote:
>> Hi!
>>
>> Yes, I did! Had to look up a conversation between me and the Tinker
>> developers about precisely this.
>>
>> The values are indeed not the original ones, but rather developed internally
>> by Tinker people so to minimise differences between analytical surface areas
>> and GB, given the HCT-algorithm and using per-atom rather than per-pair scale
>> factors. The values have not been published anywhere as such but "have been
>> used by others and seem fairly robust", according to Tinker developers.
>>
>> In the light of all other approximations introduced with implicit solvent,
>> the differences in results should be minor.
>>
>> Of course this needs to be properly documented, and it was very good that
>> some light was shed on this.
>>
>
> Great, thanks for clarifying all of this! I will make a note to adjust the
> documentation. At the moment, it sounds as if one should expect the exact HCT
> pairwise scaling method, which is obviously not the case.
>
> -Justin
>
>> /Per
>>
>>
>> 6 jul 2011 kl. 04:29 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:
>>
>>>
>>> Per Larsson wrote:
>>>> Hi! I did some digging and think I can clarify at least the first
>>>> question. Sorry for the confusion with regard to the earlier post. What
>>>> is specified in the gbsa.itp file under the gbr column is indeed
>>>> vdW-radii. These are used to compute Born radii, as the manual says. The
>>>> dielectric offset is subtracted from the vdW radii, as this has been
>>>> shown to improve the agreement between PB and GB calculations (see eg.
>>>> the OBC-paper, Onufriev, Bashford and Case, Proteins, 55, 383-394). For
>>>> the second question, I am a little confused myself now. The values found
>>>> in the gbsa.itp-file are exactly those found in the Tinker package (in
>>>> the ksolv.f-routine), which also cites the same reference. Hmm...I'll be
>>>> back again for this one.
>>> Have you uncovered anything? I've tried contacting the Tinker developers
>>> but have received no response. I found the routine (in Tinker's born.f)
>>> that utilizes the values, but I still have no idea where they come from or
>>> why they're fixed for a given atom type rather than a given pair.
>>>
>>> -Justin
>>>
>>> -- ========================================
>>>
>>> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
>>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 6 Jul 2011 14:52:47 +0200
> From: Singh <raghavbioinfo at gmail.com>
> Subject: Re: [gmx-users] Simulation of Primed DNA
> To: gmx-users at gromacs.org
> Message-ID: <04C1557F-4654-4C30-9509-2011D5CF8294 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi all,
>
> As per Justin's suggestion , I have created a rtp entry for primed THY residue..which is like this ..
>
> [ DT5P ]
> [ atoms ]
> H5T HO 0.44220 1
> O5' O -0.63180 2
> C5' CT -0.00690 3
> H5'1 H1 0.07540 4
> H5'2 H1 0.07540 5
> C4' CT 0.16290 6
> H4' H1 0.11760 7
> O4' OS -0.36910 8
> C1' CT 0.06800 9
> H1' H2 0.18040 10
> N1 N* -0.02390 11
> C6 CM -0.22090 12
> H6 H4 0.26070 13
> C5 CM 0.00250 14
> C7 CT -0.22690 15
> H71 HC 0.07700 16
> H72 HC 0.07700 17
> H73 HC 0.07700 18
> C4 C 0.51940 19
> O4 O -0.55630 20
> N3 NA -0.43400 21
> H3 H 0.34200 22
> C2 C 0.56770 23
> O2 O -0.58810 24
> C3' CT 0.07130 25
> H3' H1 0.09850 26
> C2' CT -0.08540 27
> H2'1 HC 0.07180 28
> H2'2 HC 0.07180 29
> O3' OS -0.52320 30
> P P 1.16590 31
> O1P O2 -0.77610 32
> O2P O2 -0.77610 33
> O3P O2 -0.77610 34
> [ bonds ]
> O5' P
> O5' C5'
> C5' H5'1
> C5' H5'2
> C5' C4'
> C4' H4'
> C4' O4'
> C4' C3'
> O4' C1'
> C1' H1'
> C1' N1
> C1' C2'
> N1 C6
> N1 C2
> C6 H6
> C6 C5
> C5 C7
> C5 C4
> C7 H71
> C7 H72
> C7 H73
> C4 O4
> C4 N3
> N3 H3
> N3 C2
> C2 O2
> C3' H3'
> C3' C2'
> C3' O3'
> C2' H2'1
> C2' H2'2
> [ impropers ]
> C2 C6 N1 C1'
> C4 C6 C5 C7
> N1 N3 C2 O2
> C5 N3 C4 O4
> C4 C2 N3 H3
> N1 C5 C6 H6
>
> and the THY with terminal Phosphate group is...
>
> ATOM 1 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00 O
> ATOM 2 C5' DT A 1 -4.975 -5.193 -26.943 1.00 0.00 C
> ATOM 3 1H5' DT A 1 -4.594 -5.667 -27.848 1.00 0.00 H
> ATOM 4 2H5' DT A 1 -5.809 -5.781 -26.560 1.00 0.00 H
> ATOM 5 C4' DT A 1 -3.861 -5.152 -25.898 1.00 0.00 C
> ATOM 6 H4' DT A 1 -3.531 -6.170 -25.685 1.00 0.00 H
> ATOM 7 O4' DT A 1 -2.738 -4.387 -26.383 1.00 0.00 O
> ATOM 8 C1' DT A 1 -2.272 -3.512 -25.342 1.00 0.00 C
> ATOM 9 H1' DT A 1 -1.204 -3.694 -25.215 1.00 0.00 H
> ATOM 10 N1 DT A 1 -2.478 -2.073 -25.683 1.00 0.00 N
> ATOM 11 C6 DT A 1 -3.733 -1.556 -25.872 1.00 0.00 C
> ATOM 12 H6 DT A 1 -4.556 -2.210 -26.150 1.00 0.00 H
> ATOM 13 C2 DT A 1 -1.358 -1.256 -25.798 1.00 0.00 C
> ATOM 14 O2 DT A 1 -0.205 -1.685 -25.775 1.00 0.00 O
> ATOM 15 N3 DT A 1 -1.613 0.096 -25.966 1.00 0.00 N
> ATOM 16 H3 DT A 1 -0.819 0.705 -26.089 1.00 0.00 H
> ATOM 17 C4 DT A 1 -2.857 0.699 -25.989 1.00 0.00 C
> ATOM 18 O4 DT A 1 -2.954 1.918 -26.111 1.00 0.00 O
> ATOM 19 C5 DT A 1 -3.955 -0.231 -25.855 1.00 0.00 C
> ATOM 20 C7 DT A 1 -5.368 0.283 -25.580 1.00 0.00 C
> ATOM 21 H71 DT A 1 -5.381 1.373 -25.594 1.00 0.00 H
> ATOM 22 H72 DT A 1 -5.685 -0.067 -24.597 1.00 0.00 H
> ATOM 23 H73 DT A 1 -6.051 -0.098 -26.340 1.00 0.00 H
> ATOM 24 C2' DT A 1 -2.985 -4.008 -24.085 1.00 0.00 C
> ATOM 25 2H2' DT A 1 -2.460 -4.883 -23.698 1.00 0.00 H
> ATOM 26 1H2' DT A 1 -3.043 -3.243 -23.310 1.00 0.00 H
> ATOM 27 C3' DT A 1 -4.324 -4.508 -24.586 1.00 0.00 C
> ATOM 28 H3' DT A 1 -4.981 -3.657 -24.744 1.00 0.00 H
> ATOM 29 O3' DT A 1 -4.947 -5.483 -23.741 1.00 0.00 O
> ATOM 30 P DT A 1 -6.751 -3.677 -28.479 1.00 0.00 P
> ATOM 31 O1P DT A 1 -7.056 -2.218 -28.645 1.00 0.00 O
> ATOM 32 O2P DT A 1 -7.982 -4.394 -28.010 1.00 0.00 O1-
> ATOM 33 O3P DT A 1 -6.283 -4.285 -29.883 1.00 0.00 O
>
>
> ...it started creating top and Gro files but.. when I checked visually by VMD i found that in Gro file an H is placed between CH2O and PHOSPHATE group while in my pdb it's a proper terminal... like , -CH2O-PO3..?
>
> Can anyone suggest me any further changes I am supposed to made in these files !
>
> Raghav
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 06 Jul 2011 09:07:47 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Simulation of Primed DNA
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E145E23.70307 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Singh wrote:
>> Hi all,
>>
>> As per Justin's suggestion , I have created a rtp entry for primed THY residue..which is like this ..
>>
>> [ DT5P ]
>> [ atoms ]
>> H5T HO 0.44220 1
>> O5' O -0.63180 2
>> C5' CT -0.00690 3
>> H5'1 H1 0.07540 4
>> H5'2 H1 0.07540 5
>> C4' CT 0.16290 6
>> H4' H1 0.11760 7
>> O4' OS -0.36910 8
>> C1' CT 0.06800 9
>> H1' H2 0.18040 10
>> N1 N* -0.02390 11
>> C6 CM -0.22090 12
>> H6 H4 0.26070 13
>> C5 CM 0.00250 14
>> C7 CT -0.22690 15
>> H71 HC 0.07700 16
>> H72 HC 0.07700 17
>> H73 HC 0.07700 18
>> C4 C 0.51940 19
>> O4 O -0.55630 20
>> N3 NA -0.43400 21
>> H3 H 0.34200 22
>> C2 C 0.56770 23
>> O2 O -0.58810 24
>> C3' CT 0.07130 25
>> H3' H1 0.09850 26
>> C2' CT -0.08540 27
>> H2'1 HC 0.07180 28
>> H2'2 HC 0.07180 29
>> O3' OS -0.52320 30
>> P P 1.16590 31
>> O1P O2 -0.77610 32
>> O2P O2 -0.77610 33
>> O3P O2 -0.77610 34
>> [ bonds ]
>> O5' P
>> O5' C5'
>> C5' H5'1
>> C5' H5'2
>> C5' C4'
>> C4' H4'
>> C4' O4'
>> C4' C3'
>> O4' C1'
>> C1' H1'
>> C1' N1
>> C1' C2'
>> N1 C6
>> N1 C2
>> C6 H6
>> C6 C5
>> C5 C7
>> C5 C4
>> C7 H71
>> C7 H72
>> C7 H73
>> C4 O4
>> C4 N3
>> N3 H3
>> N3 C2
>> C2 O2
>> C3' H3'
>> C3' C2'
>> C3' O3'
>> C2' H2'1
>> C2' H2'2
>> [ impropers ]
>> C2 C6 N1 C1'
>> C4 C6 C5 C7
>> N1 N3 C2 O2
>> C5 N3 C4 O4
>> C4 C2 N3 H3
>> N1 C5 C6 H6
>>
>> and the THY with terminal Phosphate group is...
>>
>> ATOM 1 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00 O
>> ATOM 2 C5' DT A 1 -4.975 -5.193 -26.943 1.00 0.00 C
>> ATOM 3 1H5' DT A 1 -4.594 -5.667 -27.848 1.00 0.00 H
>> ATOM 4 2H5' DT A 1 -5.809 -5.781 -26.560 1.00 0.00 H
>> ATOM 5 C4' DT A 1 -3.861 -5.152 -25.898 1.00 0.00 C
>> ATOM 6 H4' DT A 1 -3.531 -6.170 -25.685 1.00 0.00 H
>> ATOM 7 O4' DT A 1 -2.738 -4.387 -26.383 1.00 0.00 O
>> ATOM 8 C1' DT A 1 -2.272 -3.512 -25.342 1.00 0.00 C
>> ATOM 9 H1' DT A 1 -1.204 -3.694 -25.215 1.00 0.00 H
>> ATOM 10 N1 DT A 1 -2.478 -2.073 -25.683 1.00 0.00 N
>> ATOM 11 C6 DT A 1 -3.733 -1.556 -25.872 1.00 0.00 C
>> ATOM 12 H6 DT A 1 -4.556 -2.210 -26.150 1.00 0.00 H
>> ATOM 13 C2 DT A 1 -1.358 -1.256 -25.798 1.00 0.00 C
>> ATOM 14 O2 DT A 1 -0.205 -1.685 -25.775 1.00 0.00 O
>> ATOM 15 N3 DT A 1 -1.613 0.096 -25.966 1.00 0.00 N
>> ATOM 16 H3 DT A 1 -0.819 0.705 -26.089 1.00 0.00 H
>> ATOM 17 C4 DT A 1 -2.857 0.699 -25.989 1.00 0.00 C
>> ATOM 18 O4 DT A 1 -2.954 1.918 -26.111 1.00 0.00 O
>> ATOM 19 C5 DT A 1 -3.955 -0.231 -25.855 1.00 0.00 C
>> ATOM 20 C7 DT A 1 -5.368 0.283 -25.580 1.00 0.00 C
>> ATOM 21 H71 DT A 1 -5.381 1.373 -25.594 1.00 0.00 H
>> ATOM 22 H72 DT A 1 -5.685 -0.067 -24.597 1.00 0.00 H
>> ATOM 23 H73 DT A 1 -6.051 -0.098 -26.340 1.00 0.00 H
>> ATOM 24 C2' DT A 1 -2.985 -4.008 -24.085 1.00 0.00 C
>> ATOM 25 2H2' DT A 1 -2.460 -4.883 -23.698 1.00 0.00 H
>> ATOM 26 1H2' DT A 1 -3.043 -3.243 -23.310 1.00 0.00 H
>> ATOM 27 C3' DT A 1 -4.324 -4.508 -24.586 1.00 0.00 C
>> ATOM 28 H3' DT A 1 -4.981 -3.657 -24.744 1.00 0.00 H
>> ATOM 29 O3' DT A 1 -4.947 -5.483 -23.741 1.00 0.00 O
>> ATOM 30 P DT A 1 -6.751 -3.677 -28.479 1.00 0.00 P
>> ATOM 31 O1P DT A 1 -7.056 -2.218 -28.645 1.00 0.00 O
>> ATOM 32 O2P DT A 1 -7.982 -4.394 -28.010 1.00 0.00 O1-
>> ATOM 33 O3P DT A 1 -6.283 -4.285 -29.883 1.00 0.00 O
>>
>>
>> ...it started creating top and Gro files but.. when I checked visually by VMD i found that in Gro file an H is placed between CH2O and PHOSPHATE group while in my pdb it's a proper terminal... like , -CH2O-PO3..?
>>
>> Can anyone suggest me any further changes I am supposed to made in these files !
>>
>
> I don't see how this worked in the first place. You've defined a residue named
> "DT5P" but then expect that to be mapped onto "DT" (which it should not). Are
> you reconstructing H positions via an .hdb entry as well? I suspect you have to
> be, due to the absence of H5T, which is in the .rtp entry but not the .pdb
> coordinates. If an H atom is being placed strangely, then probably you've not
> assigned the correct geometry in the .hdb entry. See the manual.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> --
> gmx-users mailing list
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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