Re: [gmx-users] Query regarding do_dssp program
On 1/15/20 12:27 AM, Sundari wrote: 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. Without access to the coordinate file, there's nothing I can tell you. If you want to send me that snapshot off-list, I can probably take a quick look and see if I can get to the bottom of it. -Justin 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. -- == 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.
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
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.
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
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.
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.
Re: [gmx-users] Query regarding do_dssp program
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.
