Re: [gmx-users] Query regarding do_dssp program
I tried all the options.. I load gro file instead of xtc. At zero frame I gave representations new cartoon + secondary structure.. then I calculate sec str details by going on vmd timeline. I don't know what I am missing.. I am doing the same which I used all the time. Because these are two totally different secondary structures that's why I was worrying.. because these are major structures one reports so Very important to resolve this issue. On Wednesday, January 15, 2020, Justin Lemkul wrote: > > > On 1/13/20 9:15 AM, Sundari wrote: > >> Yes, Sir, I made the gro file for a particular time by using "gmx >> trjconv" command ( also checked with -pbc mol, whole, no_jump options ) >> but every time the 2ndary structure visualization in vmd is different from >> dssp sequence of residues in gromacs. Fox example in my protein dssp shows >> 8 residues making beta-sheets but when I load that particular time frame >> in >> vmd for visualizing the structure, these 8 residues showing 5-helix >> structure. >> >> Please suggest something. >> > > I'm afraid I can't. Those are two completely different hydrogen bonding > patterns and I can't imagine how the algorithms would differ so > dramatically. I have seen VMD render coils for helices and sheets but never > a totally different secondary structure. Be sure you're telling VMD to > re-compute structures and re-color the secondary structure elements at > every snapshot for trajectory visualization, otherwise it will render > everything the same as the initial frame, which will obviously be wrong in > the case of large structural changes. > > -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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding do_dssp program
Yes, Sir, I made the gro file for a particular time by using "gmx trjconv" command ( also checked with -pbc mol, whole, no_jump options ) but every time the 2ndary structure visualization in vmd is different from dssp sequence of residues in gromacs. Fox example in my protein dssp shows 8 residues making beta-sheets but when I load that particular time frame in vmd for visualizing the structure, these 8 residues showing 5-helix structure. Please suggest something. On Mon, Jan 13, 2020 at 7:01 PM Justin Lemkul wrote: > > > On 1/13/20 7:22 AM, Sundari wrote: > > Hello Dear, > > > > Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd > > use "stride" algorithm for secondary structure determination. > > But the expected error in the two algorithms should not be more than 5% > > according to the literature. Here, In my case, the structure contains a > lot > > of beta-sheets by dssp and that sequence in vmd is showing 5-helix > instead > > of beta-sheets. I am in a confusion now because I want the snapshots of > the > > structures obtained by gromacs dssp. > > Are you sure you're looking at the same snapshots? Those are wildly > different structures. I have had VMD show coils for helices and strands > before, but never any disagreement to this extent. > > -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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding do_dssp program
Hello Dear, Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd use "stride" algorithm for secondary structure determination. But the expected error in the two algorithms should not be more than 5% according to the literature. Here, In my case, the structure contains a lot of beta-sheets by dssp and that sequence in vmd is showing 5-helix instead of beta-sheets. I am in a confusion now because I want the snapshots of the structures obtained by gromacs dssp. Can you please suggest which algorithm should I use for 2ndary structure or there is any way to animate secondary structure in vmd according to dssp algorithm. Best regards, Sundari On Mon, Jan 13, 2020 at 1:37 PM Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi, > VMD and dssp may use a slightly different criteria to define a beta > sheet. > First I will check in literature if the criteria are the same. > In some case, it occur that the the atom types (e.i H) are not properly > recognized by the software, > and thus secondary structure element can not be determined. > Best regards > Alessandra > > > > On Sat, Jan 11, 2020 at 6:23 PM Sundari wrote: > > > Dear Gromacs Users, > > > > I have a big query regarding the "do_dssp" tool of gromacs-5.1.2. > > Whenever I calculate the protein secondary structure by "gmx do_dssp" , > it > > shows a significant amount of beta sheet structures. But when I load the > > same trajectory file in VMD for visualization of the secondary structure > it > > does not show any beta-sheet structures. > > > > Please, anyone, clarify the issue. > > > > Thank you in advance, > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Query regarding do_dssp program
Dear Gromacs Users, I have a big query regarding the "do_dssp" tool of gromacs-5.1.2. Whenever I calculate the protein secondary structure by "gmx do_dssp" , it shows a significant amount of beta sheet structures. But when I load the same trajectory file in VMD for visualization of the secondary structure it does not show any beta-sheet structures. Please, anyone, clarify the issue. Thank you in advance, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Doubt in nmol tool
Dear Gromacs users, Can anyone explain about -nmol (number of molecules ) option in gmx gyrate tool. According to me I have 3 peptide chains in my simulation box and I am using " -nmol 3". Is it correct what I have used for this option? Regards Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding MM/GBSA method implemented in the GROMACS package
Hi, Is there any other way for example calculation of binding energy by my existed files (normal MD .trr and .edr files) generated by gromacs instead of restart a simulation. Because currently I am not familiar with the umbrella sampling and have urgent need of energies. Please suggest any idea. sundari On Fri, Sep 28, 2018 at 8:47 PM rose rahmani wrote: > Hi, > > You can calculate adsorption energy by umbrella sampling. > http://www.mdtutorials.com/gmx/umbrella/index.html > .edr just gives you the interaction energy not adsorption energy and > distance. > > Rose > > On Fri, Sep 28, 2018 at 6:37 PM Sundari wrote: > > > Dear Gromacs users, > > > > I want to calculate Binding energy between the protein and the carbon > nano > > tube. Is there any way to do that by gromacs commands. > > As I only have .xtc and .tpr files from gromacs. > > > > Please suggest me any idea or any article so that based on trajectories > > (xtc or trr) how one can get these binding energies. > > > > Regards, > > Sundar > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding MM/GBSA method implemented in the GROMACS package
Dear Gromacs users, I want to calculate Binding energy between the protein and the carbon nano tube. Is there any way to do that by gromacs commands. As I only have .xtc and .tpr files from gromacs. Please suggest me any idea or any article so that based on trajectories (xtc or trr) how one can get these binding energies. Regards, Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding MM/GBSA method implemented in the GROMACS package
Dear Gromacs users, I want to calculate Binding energy between the protein and the carbon nano tube. Is there any way to do that by gromacs commands. As I only have .xtc and .tpr files from gromacs. Please suggest me any idea or any article so that based on trajectories (xtc or trr) how one can get these binding energies. Regards, Sundar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Increase of 5-helix count
Kindly look at my query.. Thank you! On Mon, Jun 11, 2018 at 5:39 PM, Sundari wrote: > Dear gromacs users, > > I am running a simulation of three alpha helical peptides with a carbon > nano tube in a simulation box. Actually I am following a paper and want to > reproduce the results. > > In my simulation every time there is a sudden increase of 5-helix count, > means most of the alpha helix converted into 5-helix. > > I am using gromacs version 5.1.2. and paper used gromacs version 4. So I > am confuse is this difference I am getting because of Gromacs version or > something else? > And 5-helix is not counted in total secondary structure count. > (scount.xvg) > please suggest something. > > > Thank you in advance.. > > > > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Increase of 5-helix count
Dear gromacs users, I am running a simulation of three alpha helical peptides with a carbon nano tube in a simulation box. Actually I am following a paper and want to reproduce the results. In my simulation every time there is a sudden increase of 5-helix count, means most of the alpha helix converted into 5-helix. I am using gromacs version 5.1.2. and paper used gromacs version 4. So I am confuse is this difference I am getting because of Gromacs version or something else? And 5-helix is not counted in total secondary structure count. (scount.xvg) please suggest something. Thank you in advance.. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD temperature_space
Hello Guys, Kindly suggest me something about my doubt. On Thu, May 3, 2018 at 5:19 PM, Sundari <sundi6...@gmail.com> wrote: > Hello, > > I got the continuous trajectories by using demux. But now I am confused in > getting potential energy distribution of a single replica (similarly time > evolution of a replica (say replica_1) in temperature space). > I used edr file of original production data files, but I am not getting > what I want. I am attaching the temp.xvg file of one replica (say T= 315K > replica) > > Thank You.. > > On Thu, May 3, 2018 at 5:02 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> It sounds like you just want to use the original data, which you had >> before >> you ran the demux script. >> >> Mark >> >> On Thu, May 3, 2018 at 1:28 PM Sundari <sundi6...@gmail.com> wrote: >> >> > Dear gromacs users, >> > >> > can anyone please suggest me that how we get the time evolution of a >> > replica (say replica_1) in temperature space and time courses of >> potential >> > energy of each replica( one way is md.edr file??) >> > As according to GROMACS tutorial, I used demux.pl script and got two >> files >> > replica_index.xvg and replica_temp.xvg. But I want to analyse a single >> > replica trajectory in all temperatures ( temp. on y-axis) >> > >> > >> > Thank you in advance.. >> > >> > Sundari >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD temperature_space
Hello, I got the continuous trajectories by using demux. But now I am confused in getting potential energy distribution of a single replica (similarly time evolution of a replica (say replica_1) in temperature space). I used edr file of original production data files, but I am not getting what I want. I am attaching the temp.xvg file of one replica (say T= 315K replica) Thank You.. On Thu, May 3, 2018 at 5:02 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > It sounds like you just want to use the original data, which you had before > you ran the demux script. > > Mark > > On Thu, May 3, 2018 at 1:28 PM Sundari <sundi6...@gmail.com> wrote: > > > Dear gromacs users, > > > > can anyone please suggest me that how we get the time evolution of a > > replica (say replica_1) in temperature space and time courses of > potential > > energy of each replica( one way is md.edr file??) > > As according to GROMACS tutorial, I used demux.pl script and got two > files > > replica_index.xvg and replica_temp.xvg. But I want to analyse a single > > replica trajectory in all temperatures ( temp. on y-axis) > > > > > > Thank you in advance.. > > > > Sundari > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD temperature_space
Dear gromacs users, can anyone please suggest me that how we get the time evolution of a replica (say replica_1) in temperature space and time courses of potential energy of each replica( one way is md.edr file??) As according to GROMACS tutorial, I used demux.pl script and got two files replica_index.xvg and replica_temp.xvg. But I want to analyse a single replica trajectory in all temperatures ( temp. on y-axis) Thank you in advance.. Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Secondary structure propensity.
Thanks a lot ... On Sun, Feb 18, 2018 at 9:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/18/18 6:05 AM, Sundari wrote: > >> Thank You :) >> >> I have a little doubt now. If I want total percentage of all 8 secondary >> structures separately i.e SS (%) than I can get this by simply averaging >> the propensities of ss ? >> >> > No, that will give you a constant number. All residues have to be in one > type of secondary structure (including coil) and they can only interconvert > between them. If you do any sort of averaging over the 8 types, you get a > constant. The calculation I gave before will do what you want. > > -Justin > > > >> >> On Fri, Feb 16, 2018 at 6:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: >>> >>> Hello, >>>> >>>> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , >>>> it >>>> contains the required information. >>>> >>>> Only indirectly, but scount.xvg has all that is needed, the number of >>> residues in a given secondary structure as a function of time. From that, >>> percentage over time is a trivial scripting task, [(# in SS) / (# of >>> residues)]*100. >>> >>> -Justin >>> >>> Regards, >>> >>>> S. Borkotoky >>>> >>>> On Fri, Feb 16, 2018 at 1:30 PM, Sundari <sundi6...@gmail.com> wrote: >>>> >>>> Dear gromacs users, >>>> >>>>> can any one please tell me that how we get the secondary structure >>>>> propensity or secondary structure content(%) as a function of >>>>> simulation >>>>> time. >>>>> >>>>> I used "gmx do_dssp" but it gives me number of residues forming the >>>>> secondary structure vs simulation time. is it same thing or something >>>>> different? >>>>> >>>>> Thank you in advance.. >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at http://www.gromacs.org/ >>>>> Support/Mailing_Lists/GMX-Users_List before posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> >>>>> >>>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Secondary structure propensity.
Thank You :) I have a little doubt now. If I want total percentage of all 8 secondary structures separately i.e SS (%) than I can get this by simply averaging the propensities of ss ? On Fri, Feb 16, 2018 at 6:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: > >> Hello, >> >> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , >> it >> contains the required information. >> > > Only indirectly, but scount.xvg has all that is needed, the number of > residues in a given secondary structure as a function of time. From that, > percentage over time is a trivial scripting task, [(# in SS) / (# of > residues)]*100. > > -Justin > > Regards, >> >> S. Borkotoky >> >> On Fri, Feb 16, 2018 at 1:30 PM, Sundari <sundi6...@gmail.com> wrote: >> >> Dear gromacs users, >>> >>> can any one please tell me that how we get the secondary structure >>> propensity or secondary structure content(%) as a function of simulation >>> time. >>> >>> I used "gmx do_dssp" but it gives me number of residues forming the >>> secondary structure vs simulation time. is it same thing or something >>> different? >>> >>> Thank you in advance.. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] SS Content?
my problem resolved :) Thank you On Sun, Feb 18, 2018 at 4:22 PM, Sundari <sundi6...@gmail.com> wrote: > Dear gromacs users, > > can any one please tell me that how we get the secondary structure > propensity or secondary structure content(%) as a function of simulation > time. > > I used "gmx do_dssp" but it gives me number of residues forming the > secondary structure vs simulation time. is it same thing or something > different? > > Thank you in advance.. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or something different? Thank you in advance.. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Secondary structure propensity.
Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or something different? Thank you in advance.. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Structures after Dihedral principle component analysis(dPCA)
Dear all I have plotted the Free Energy Landscapes(2D) of proteins from First two principal components as used by GROMACS, But after that I am confused how to do clustering on PCA surface or I want to know how to calculate the structure of protein corresponding to lowest free energy in FELs. Is there any gromacs tool available to get pdb for lowest energy structure after PCA calculation? Because as per my knowledge "gmx cluster" works with RMS deviations. Please, anyone suggest me something ( any hint or link) to resolve this problem. Thank You in advance! (Dhanyawad) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem with NPT simulation
Dear all, I am doing a protein simulation. After NVT equilibration, I tried to do NPT but everytime I got this error :- --- Program gmx grompp, VERSION 5.1.2 Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line: 1806 Fatal error: [ file posre.itp, line 5 ]: Atom index (259) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I generated posre.itp file using "gmx genrestr -f solv.gro -o " . please, anyone help me to understand this grompp error. Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Secondary structure content
Thank you all.. On Saturday, September 9, 2017, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/9/17 1:43 PM, nidhi wrote: > >> Thank you :) >> Can you please suggest me than what's the last line of scount.xvg file >> indicates? >> It is ss(%), what does it mean? Which kind of secondary structure >> percentage is this? >> > > It should be the fraction of residues of each type of structure. > > -Justin > > Thank you for your time and help.. >> >> On 9 Sep 2017 7:03 p.m., "Justin Lemkul" <jalem...@vt.edu> wrote: >> >> >>> On 9/9/17 9:30 AM, Smith, Micholas D. wrote: >>> >>> If i remember correctly the DSSP plot should be something like residue # >>>> on y-axis, and time on the x-axis, then it is normally a color plot of >>>> what >>>> secondary structure each residue is in at that time point. Secondary >>>> structure content (%) vs time sounds more like a single plot of the >>>> fraction of residues (%) of residues at each time point that are not in >>>> a >>>> 'coil' state. >>>> >>>> >>>> That's just the ss.xpm file. The scount.xvg has a time series of the >>> number of residues in each type of secondary structure over time. To the >>> OP's question, it is not a percentage, it is the number of residues, from >>> which computing percentage is trivial based on the number of total >>> residues. >>> >>> -Justin >>> >>> Hope that makes sense. >>> >>>> === >>>> Micholas Dean Smith, PhD. >>>> Post-doctoral Research Associate >>>> University of Tennessee/Oak Ridge National Laboratory >>>> Center for Molecular Biophysics >>>> >>>> >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of >>>> Sundari < >>>> sundi6...@gmail.com> >>>> Sent: Saturday, September 09, 2017 5:48 AM >>>> To: gromacs.org_gmx-users@maillist.sys.kth.se >>>> Subject: [gmx-users] Secondary structure content >>>> >>>> Dear all, >>>> I am confused with 'dssp' output graph i.e "number of residues vs time". >>>> Is >>>> it also called "secondary structure content(%) vs time" ?? Or it is >>>> different term? >>>> >>>> please, anyone help me to solve this confusion or send me any link >>>> contained proper definition of these two. >>>> >>>> Thanks in advance >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at http://www.gromacs.org/Support >>>> /Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> >>>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Secondary structure content
Dear all, I am confused with 'dssp' output graph i.e "number of residues vs time". Is it also called "secondary structure content(%) vs time" ?? Or it is different term? please, anyone help me to solve this confusion or send me any link contained proper definition of these two. Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Number of Contacts
If anyone have Idea. kindly suggest. On Wednesday, June 28, 2017, Sundari <sundi6...@gmail.com> wrote: > Hi, > > I used the following command.. > gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od > minidist.xvg -on numb_count -d 0.65 > By doing this I got this numb_count.xvg graph here > > https://drive.google.com/open?id=0B99qIEZlZSXfVnQxY3JsUm1rRnc > > In this number of contacts varying up to 500 which is impossible for my > small peptide chain ( two chains in a simulation box and both are seven > residue long ). From this I concluded that may be number is so high, > because in command line -d 0.65 is not the COM distance. So than I used > this > > gmx select -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -select 'group > "sd-1" and within 0.65 of com of group "sd-2"' -os size.xvg > > Where group sd-1 and sd-2 are the side-chain atom index for 1st and 2nd > peptide chain. The output by this command is in below link > > > https://drive.google.com/open?id=0B99qIEZlZSXfRDlXN3RaVFROc2s > > here, output is a size.xvg file which is looking something feasible. I am > not sure is that output contains number of inter peptide contacts which I > needed or this is something else as the name suggested "size.xvg". Please > clear my confusion. > > Thank you! > > Sundari > > > > On Wed, Jun 28, 2017 at 6:55 AM, Dallas Warren <dallas.war...@monash.edu > <javascript:_e(%7B%7D,'cvml','dallas.war...@monash.edu');>> wrote: > >> First thing you should do when asking for help, is specify exactly >> what you have have done (that includes the command line and output), >> and then why it is "wrong result". >> Catch ya, >> >> Dr. Dallas Warren >> Drug Delivery, Disposition and Dynamics >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3052 >> dallas.war...@monash.edu >> <javascript:_e(%7B%7D,'cvml','dallas.war...@monash.edu');> >> - >> When the only tool you own is a hammer, every problem begins to resemble >> a nail. >> >> >> On 28 June 2017 at 01:27, Sundari chaudhary <sundi6...@gmail.com >> <javascript:_e(%7B%7D,'cvml','sundi6...@gmail.com');>> wrote: >> > Dear all, >> > >> > I want to calculate the number of inter-peptide and intra-peptide >> > side-chain–side-chain contacts and the criteria to form a contact is >> that: >> > the distance between the centers of mass of two residues is less than a >> > specified distance. I tried gmx mindist and gmx distance command lines >> but >> > i got wrong results. >> > >> > Please suggest me right command line to do this analysis. >> > >> > >> > Thank you! >> > >> > Sundari >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org >> <javascript:_e(%7B%7D,'cvml','gmx-users-requ...@gromacs.org');>. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org >> <javascript:_e(%7B%7D,'cvml','gmx-users-requ...@gromacs.org');>. > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Number of Contacts
Hi, I used the following command.. gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od minidist.xvg -on numb_count -d 0.65 By doing this I got this numb_count.xvg graph here https://drive.google.com/open?id=0B99qIEZlZSXfVnQxY3JsUm1rRnc In this number of contacts varying up to 500 which is impossible for my small peptide chain ( two chains in a simulation box and both are seven residue long ). From this I concluded that may be number is so high, because in command line -d 0.65 is not the COM distance. So than I used this gmx select -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -select 'group "sd-1" and within 0.65 of com of group "sd-2"' -os size.xvg Where group sd-1 and sd-2 are the side-chain atom index for 1st and 2nd peptide chain. The output by this command is in below link https://drive.google.com/open?id=0B99qIEZlZSXfRDlXN3RaVFROc2s here, output is a size.xvg file which is looking something feasible. I am not sure is that output contains number of inter peptide contacts which I needed or this is something else as the name suggested "size.xvg". Please clear my confusion. Thank you! Sundari On Wed, Jun 28, 2017 at 6:55 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > First thing you should do when asking for help, is specify exactly > what you have have done (that includes the command line and output), > and then why it is "wrong result". > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 28 June 2017 at 01:27, Sundari chaudhary <sundi6...@gmail.com> wrote: > > Dear all, > > > > I want to calculate the number of inter-peptide and intra-peptide > > side-chain–side-chain contacts and the criteria to form a contact is > that: > > the distance between the centers of mass of two residues is less than a > > specified distance. I tried gmx mindist and gmx distance command lines > but > > i got wrong results. > > > > Please suggest me right command line to do this analysis. > > > > > > Thank you! > > > > Sundari > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Number of Contacts
Dear all, I want to calculate the number of inter-peptide and intra-peptide side-chain–side-chain contacts and the criteria to form a contact is that: the distance between the centers of mass of two residues is less than a specified distance. I tried gmx mindist and gmx distance command lines but i got wrong results. Please suggest me right command line to do this analysis. Thank you! Sundari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
