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-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 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 <ros...@kth.se> > Subject: Re: [gmx-users] Register > To: Saeid Akbarshahi <saeidakbarsh...@yahoo.com>, Discussion list for > GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e143a7c.20...@kth.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > You can only register from the website: > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Rossen > > > ------------------------------ > > Message: 2 > Date: Wed, 06 Jul 2011 07:00:11 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] make a new bond in VERSION 4.5.4 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e14403b.1020...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > 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" <jalem...@vt.edu> > Subject: Re: [gmx-users] Questions about GB parameters > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e144ec1.1060...@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" <jalem...@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 >>> >>> ======================================== -- gmx-users mailing list >>> gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please >>> don't post (un)subscribe requests to the list. Use the www interface or >>> send it to gmx-users-requ...@gromacs.org. Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists >> >> > > -- > ======================================== > > 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 <raghavbioi...@gmail.com> > Subject: Re: [gmx-users] Simulation of Primed DNA > To: gmx-users@gromacs.org > Message-ID: <04c1557f-4654-4c30-9509-2011d5cf8...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] Simulation of Primed DNA > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e145e23.70...@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 > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 87, Issue 32 > ***************************************** -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
