Custom Search
-- *Thanks & Regards* *C .Sathyaseelan * *PhD Research Scholar* *C/o Dr. Thenmalarchelvi Rathinavelan* *Molecular Biophysics Lab* *Dept. of Biotechnology* *Indian Institute of Technology (IIT)* *Kandi, Hyderabad, Telangana - 502285* *Ph.No 6383836804, 8300150807* -- Disclaimer:- The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this email. Please notify the sender immediately and destroy all copies of this message and any attachments. The views expressed in this E-mail message (including the enclosure/(s) or attachment/(s) if any) are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of IIT Hyderabad. Before opening any mail and attachments please check them for viruses, malware, and the sender email address is indeed from IITH domain. IITH does not accept any liability for malware infected mails. -------------- next part -------------- A non-text attachment was scrubbed... Name: nowaterbox.png Type: image/png Size: 92301 bytes Desc: not available Url : http://lists.ambermd.org/mailman/private/amber/attachments/20201202/84aeff75 /attachment-0002.png -------------- next part -------------- A non-text attachment was scrubbed... Name: waterbox.png Type: image/png Size: 133732 bytes Desc: not available Url : http://lists.ambermd.org/mailman/private/amber/attachments/20201202/84aeff75 /attachment-0003.png ------------------------------ Message: 7 Date: Wed, 2 Dec 2020 08:53:32 +0100 From: Karl Kirschner <k.n.kirschner.gmail.com> Subject: Re: [AMBER] question about dihedral angles To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAF=D-bz-j1Y7Qp-7_frB-jzU9DBn61cxdxyYM5-jkdQmwemefA.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi, Richard, You can rotate a dihedral in tleap by using the "impose" command. Let's say you have an tleap object named "mymolecule" that is composed of several residues, and you want to rotate residue 7's atoms that are named C1, C2, C3 and C4 to 120 degrees, then the following command should work: impose mymolecule {7} { {C1 C2 C3 C4 120.0} } Note that it becomes a bit unclear if you have rotating a dihedral is between two residues. Then you indicate the lower residue number, and start the sequence with it's atom names. In the Amber20's manual, you can find additional examples on page 242 (subsection entitled "Procedures for building oligosaccharides using the GLYCAM-06 parameters"). An alternative approach is to use PyMol, which would enable you to visually see the rotation being made and if any atomic clashes happen. To do this you need to label the atoms via their "ID" and then use the command "set_dihedral" (e.g. "set_dihedral ID 6, ID 7, ID 8, ID 9, 120") Using PyMol will add a few steps to your workflow since the resulting structure must be saved to a PDB-formatted file and then be loaded back into tleap. However, this approach will help maintain a precise understanding of what is structurally happening to your molecule with your manual manipulation. Furthermore, you can create a PyMol script that allows you to encode these changes and then have a reminder of exactly what you did for your model building, increasing the reproducibility of the workflow if needed later. Bests, Karl On Wed, Dec 2, 2020 at 3:07 AM David A Case <david.case.rutgers.edu> wrote: > On Tue, Dec 01, 2020, Gordon Richard Chalmers wrote: > > > >I have a quick question as to how AmberTools20, tleap, or cpptraj > >rotates the molecule about a phi or psi dihedral angle. > > The world's experts on this subject are right in your backyard: check > with Rob Woods or Lachele Foley, who probably have the longest > institutional memory about this. > > The basic problem is that just saying you want to rotate about an > angle is not enough information. One also needs to specify which atoms (i.e. > which "side" of the torsion) should be moved. But the tleap syntax > doesn't include this, and it can be rather difficult to understand its > internal procedures for making this decision. > > I'm less familiar with cpptraj handles this problem. > > ....dac > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 8 Date: Wed, 2 Dec 2020 08:12:38 +0000 From: Gustaf Olsson <gustaf.olsson.lnu.se> Subject: Re: [AMBER] Imaging issue in DNA - cpptraj To: AMBER Mailing List <amber.ambermd.org> Message-ID: <792960D5-71D0-4DAB-A764-F5561BC21A79.lnu.se> Content-Type: text/plain; charset="us-ascii" Short of increasing the solvent buffer to avoid jumps, trying to play around with the masks for image/autoimage seems reasonable. See what happens if you autoimage with a mask defined. Either trying to center the entire DNA or as suggested (https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small region of the DNA which should be close to the center of the box. Best regards // Gustaf On 2 Dec 2020, at 08:17, Satyaseelan C <bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote: Dear Amber users, I am facing an imaging issue during the MD simulation of a DNA duplex. Due to this, the RMSD is shooting up and falls back during the middle of the simulation. I am observing this problem for 50ns during the simulation. I used autoimage option followed by image option as below: parm prmtop trajin trajin.nc autoimage center :1-16 origin image origin center familiar center :1-32 origin image origin center familiar trajout reimage.nc go When I don't apply any imaging, the DNA strands are separated and going out of the box in some frames. But, after performing imaging, the problem is not completely resolved. Here, a stretch of DNA strand is going away and causes distortions in the structure for 50ns. I have attached the corresponding snapshots. Please suggest any alternative options to overcome this issue. Thanks in advance Sathyaseelan -- *Thanks & Regards* *C .Sathyaseelan * *PhD Research Scholar* *C/o Dr. Thenmalarchelvi Rathinavelan* *Molecular Biophysics Lab* *Dept. of Biotechnology* *Indian Institute of Technology (IIT)* *Kandi, Hyderabad, Telangana - 502285* *Ph.No 6383836804, 8300150807* -- Disclaimer:- The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this email. Please notify the sender immediately and destroy all copies of this message and any attachments. The views expressed in this E-mail message (including the enclosure/(s) or attachment/(s) if any) are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of IIT Hyderabad. Before opening any mail and attachments please check them for viruses, malware, and the sender email address is indeed from IITH domain. IITH does not accept any liability for malware infected mails. <nowaterbox.png><waterbox.png>______________________________________________ _ AMBER mailing list AMBER.ambermd.org<mailto:AMBER.ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 9 Date: Wed, 2 Dec 2020 10:23:56 +0100 From: "Dr. Anselm Horn" <anselm.horn.fau.de> Subject: Re: [AMBER] Imaging issue in DNA - cpptraj To: <amber.ambermd.org> Message-ID: <33b14e89-7927-8bc7-bfd9-2f97be4c49c9.fau.de> Content-Type: text/plain; charset="utf-8" Hi, just to add a comment: If you used iwrap=1 in your simulation input, try to use the unwrap command in cpptraj, expecially, if you are not interested in the solvent molecules: strip off these first, the do the unwrap and omit the (auto)image commands. However, you may want to use a rms fit command to obtain a trajectory better to visualize. Regards, Anselm On 12/02/2020 09:12 AM, Gustaf Olsson wrote: > Short of increasing the solvent buffer to avoid jumps, trying to play around with the masks for image/autoimage seems reasonable. > > See what happens if you autoimage with a mask defined. Either trying to center the entire DNA or as suggested (https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small region of the DNA which should be close to the center of the box. > > Best regards > // Gustaf > > > On 2 Dec 2020, at 08:17, Satyaseelan C <bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote: > > Dear Amber users, > I am facing an imaging issue during the MD simulation of > a DNA duplex. Due to this, the RMSD is shooting up and falls back > during the middle of the simulation. I am observing this problem for > 50ns during the simulation. I used autoimage option followed by image option as below: > > parm prmtop > trajin trajin.nc > autoimage > center :1-16 origin > image origin center familiar > center :1-32 origin > image origin center familiar > trajout reimage.nc > go > > When I don't apply any imaging, the DNA strands are separated and > going out of the box in some frames. But, after performing imaging, > the problem is not completely resolved. Here, a stretch of DNA strand > is going away and causes distortions in the structure for 50ns. I have > attached the corresponding snapshots. > > Please suggest any alternative options to overcome this issue. > > > Thanks in advance > Sathyaseelan > > -- > *Thanks & Regards* > > *C .Sathyaseelan * > *PhD Research Scholar* > *C/o Dr. Thenmalarchelvi Rathinavelan* *Molecular Biophysics Lab* > *Dept. of Biotechnology* *Indian Institute of Technology (IIT)* > *Kandi, Hyderabad, Telangana - 502285* *Ph.No 6383836804, 8300150807* > > -- > > > Disclaimer:- The information contained in this electronic message and > any attachments to this message are intended for the exclusive use of > the > addressee(s) and may contain proprietary, confidential or privileged > information. If you are not the intended recipient, you should not > disseminate, distribute or copy this email. Please notify the sender > immediately and destroy all copies of this message and any > attachments. The views expressed in this E-mail message (including the > enclosure/(s) or > attachment/(s) if any) are those of the individual sender, except > where the sender expressly, and with authority, states them to be the > views of IIT Hyderabad. Before opening any mail and attachments please > check them for viruses, malware, and the sender email address is indeed from IITH domain. > IITH does not accept any liability for malware infected mails. > > <nowaterbox.png><waterbox.png>________________________________________ > _______ > AMBER mailing list > AMBER.ambermd.org<mailto:AMBER.ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 10 Date: Wed, 2 Dec 2020 17:04:52 +0700 From: lomzov <lomzov.niboch.nsc.ru> Subject: Re: [AMBER] Imaging issue in DNA - cpptraj To: AMBER Mailing List <amber.ambermd.org> Message-ID: <715304c9-aa30-5df4-9098-331ebef82aa0.niboch.nsc.ru> Content-Type: text/plain; charset=windows-1252; format=flowed Hi, We were not successful to unwrap DNA duplexes using cpptraj. To solve this problem at the modeling stage, we found two solutions: 1) as suggested by Anselm using iwrap = 0, but for long-term simulations (more than 50-100 ns) water molecules and cations may go too far and this cannot be written to the old format mdcrd file. To solve this issue you can simulate with iwrap = 0 for 50 ns, and than short simulate iwrap = 1 for 5-10 ns. Sometimes it helps. 2) use very weak Cartesian restraints (0.01 kcal / mol / A) for two atoms in opposite chains with iwrap = 1. For example, for 16 bp duplex ntr = 1, restraint_wt=0.01 , restraintmask=" :8,24.C4'", This does not allow translation movement of the duplex, but becaose of low value of restraint does not change duplex conformation. If you want to analyze conformation changes, you could restart simulation every few nanoseconds (5-10 ns) using the reference file, which was obtained at previous stage stage 1: ..... -r 1.restrt -ref 0.inpcrs stage 2: ..... -r 2.restrt -ref 1.restrt stage 3: ..... -r 3.restrt -ref 2.restrt good luck! Alex On 02.12.2020 16:23, Dr. Anselm Horn wrote: > Hi, > > just to add a comment: > If you used iwrap=1 in your simulation input, try to use the unwrap > command in cpptraj, expecially, if you are not interested in the > solvent > molecules: strip off these first, the do the unwrap and omit the > (auto)image commands. > > However, you may want to use a rms fit command to obtain a trajectory > better to visualize. > > Regards, > > Anselm > > > On 12/02/2020 09:12 AM, Gustaf Olsson wrote: >> Short of increasing the solvent buffer to avoid jumps, trying to play around with the masks for image/autoimage seems reasonable. >> >> See what happens if you autoimage with a mask defined. Either trying to center the entire DNA or as suggested (https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small region of the DNA which should be close to the center of the box. >> >> Best regards >> // Gustaf >> >> >> On 2 Dec 2020, at 08:17, Satyaseelan C <bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote: >> >> Dear Amber users, >> I am facing an imaging issue during the MD simulation >> of a DNA duplex. Due to this, the RMSD is shooting up and falls back >> during the middle of the simulation. I am observing this problem for >> 50ns during the simulation. I used autoimage option followed by image option as below: >> >> parm prmtop >> trajin trajin.nc >> autoimage >> center :1-16 origin >> image origin center familiar >> center :1-32 origin >> image origin center familiar >> trajout reimage.nc >> go >> >> When I don't apply any imaging, the DNA strands are separated and >> going out of the box in some frames. But, after performing imaging, >> the problem is not completely resolved. Here, a stretch of DNA strand >> is going away and causes distortions in the structure for 50ns. I >> have attached the corresponding snapshots. >> >> Please suggest any alternative options to overcome this issue. >> >> >> Thanks in advance >> Sathyaseelan >> >> -- >> *Thanks & Regards* >> >> *C .Sathyaseelan * >> *PhD Research Scholar* >> *C/o Dr. Thenmalarchelvi Rathinavelan* *Molecular Biophysics Lab* >> *Dept. of Biotechnology* *Indian Institute of Technology (IIT)* >> *Kandi, Hyderabad, Telangana - 502285* *Ph.No 6383836804, 8300150807* >> >> -- >> >> >> Disclaimer:- The information contained in this electronic message and >> any attachments to this message are intended for the exclusive use of >> the >> addressee(s) and may contain proprietary, confidential or privileged >> information. If you are not the intended recipient, you should not >> disseminate, distribute or copy this email. Please notify the sender >> immediately and destroy all copies of this message and any >> attachments. The views expressed in this E-mail message (including >> the enclosure/(s) or >> attachment/(s) if any) are those of the individual sender, except >> where the sender expressly, and with authority, states them to be the >> views of IIT Hyderabad. Before opening any mail and attachments >> please check them for viruses, malware, and the sender email address is indeed from IITH domain. >> IITH does not accept any liability for malware infected mails. >> >> <nowaterbox.png><waterbox.png>_______________________________________ >> ________ >> AMBER mailing list >> AMBER.ambermd.org<mailto:AMBER.ambermd.org> >> http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 11 Date: Wed, 2 Dec 2020 13:27:56 +0100 From: Pavl?na Pokorn? <pokorna.pavlina.ibp.cz> Subject: Re: [AMBER] NOE analysis with cpptraj To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CACHm3M0XvrVPxXxh598wNgiSbZSjSwqWGP1We9uK19n_CaNAkA.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Daniel, thanks for Your reply. No, I don't want cpptraj to use closer of the two (or more) distances but to use their r^-6 weighted average. i.e.: to use r^-6 weighted average of all distances per frame in the mask to compute their final r^-6 weighted average over the whole trajectory to get NOE violations. What I get now is r^-6 weighted average over the whole trajectory computed for center-of-mass distances, not for r^-6 weighted averages (per frame). This leads to slightly higher values of NOE violations for multiple-mask distances with "distance type noe" than what is the correct value. Sander can be also used to analyze NOE violations and there the r^-6 weighted averaging for multiple-atom NOEs works well. Best wishes, Pavlina On Wed, Nov 25, 2020 at 4:26 PM Daniel Roe <daniel.r.roe.gmail.com> wrote: > Hi, > > Sorry for the long delay on this. So do you mean you want cpptraj to > automatically choose the closer of the two distances? If so, you can't > do that with the 'distance' command, but you might be able to get it > to work with the 'nativecontacts' command and the 'mindist' keyword. > The generated dataset with the [mindist] aspect could then be sent to > the 'stat' analysis. Disclaimer: I haven't had a chance to test it, > but that seems like it should work with those atom masks. > > -Dan > > On Mon, Oct 19, 2020 at 9:18 AM Pavl?na Pokorn? > <pokorna.pavlina.ibp.cz> > wrote: > > > > Dear all, > > > > I have a question regarding NOE analysis when using a multiple-atom > > mask with cpptraj. > > > > If I use: > > distance 117RADE_H8-41LYS_QG :117.H8 :41.HG= type noe noe_weak > > analyze statistics all out noe.dat noeout noeout.dat > > > > --> cpptraj then uses center-of-mass of :41.HG2 and :41.HG3 atoms to > > compute its r6 weighted average distance with :117.H8 instead of > treating > > each of the :41.HG* atoms individually. There is no problem if I > calculate > > NOE with equivalent command using masks which both contain only one > > hydrogen atom. > > > > So, is it possible to make cpptraj use the r6 weighted averaging > > instead > of > > center-of-mass averaging when "type noe" is specified for distance > > action with multiple atoms in the mask? Did I miss something with my > > cpptraj commands? > > > > Thank You, > > Pavlina Pokorna > > > > > > -- > > RNDr. Pavl?na Pokorn? > > *PhD student* > > Institute of Biophysics of the CAS, v. v. i. > > Kralovopolska 135, 612 65 Brno > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- *RNDr. Pavl?na Pokorn?* *PhD student* Institute of Biophysics of the CAS, v. v. i. Kralovopolska 135, 612 65 Brno ------------------------------ Message: 12 Date: Wed, 2 Dec 2020 08:51:08 -0500 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] question about dihedral angles To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20201202135108.br5y4ktxpfpbfxib.Davids-MBP.fios-router.home> Content-Type: text/plain; charset=us-ascii; format=flowed On Wed, Dec 02, 2020, Karl Kirschner wrote: > >impose mymolecule {7} { {C1 C2 C3 C4 120.0} } One point is this: the command above doesn't specific which atoms are to be *moved* in order to make the dihderal be 120 degrees. Should the program move C4 (and atoms bonded to it), or move C1 (and atoms bonded to it)? Or do something else? This may not be important in some workflows, but can be key in others. The pyMol example has the same problem. Of course, its documentation may be better in explaining what choices are made. These sorts of manipulations are a natural for NAB (aka "molecular awk"), but it has its own learning curve and documentation deficiencies. ....dac ------------------------------ Message: 13 Date: Wed, 2 Dec 2020 08:55:09 -0500 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] Imaging issue in DNA - cpptraj To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20201202135509.ndw6p5uz7zh6dqyq.Davids-MBP.fios-router.home> Content-Type: text/plain; charset=us-ascii; format=flowed On Wed, Dec 02, 2020, lomzov wrote: >1) as suggested by Anselm using iwrap = 0, but for long-term simulations >(more than 50-100 ns) water molecules and cations may go too far and >this cannot be written to the old format mdcrd file. The expectation is that you will use netcdf format for trajectory and restart files. If you need the old format mdcrd for something, then do this in cpptraj: read in the netcdf trajectory image the water ions write out the trajectory in mdcrd format ...good luck...dac ------------------------------ Message: 14 Date: Wed, 2 Dec 2020 14:03:54 +0000 From: Gordon Richard Chalmers <gordoncs.uga.edu> Subject: Re: [AMBER] question about dihedral angles To: AMBER Mailing List <amber.ambermd.org> Message-ID: <DM5PR02MB2715829462FF2DCEF9E521B1DCF30.DM5PR02MB2715.namprd02.prod.outlook. com> Content-Type: text/plain; charset="iso-8859-1" Thank you for the help in this. In a protein the phi and psi angles require 2 adjacent residues. Calculating these angles and rotating is fairly easy. It is a matter of what is rotated to agree to a PDB model starting from a linear backbone model. I will be working the angle rotations further in tleap today, a little delayed at the moment. In principle, you should rotate the entire peptide chain after or before the ith residue as these are bonded in %% phi C(i-1)-N-CA-C %% psi N-CA-C-N(i+1) The actual rotation angle about the intermediary N-CA or CA-C axis should be the dihedral angle geometrically. Maybe my own Matlab algorithms aren't correct yet, but I have checked this many times. I will try to use tleap or cpptraj instead as a check. Gordon Chalmers Department of Computer Science Complex Carbohydrate Research Center University of Georgia ________________________________ From: David A Case <david.case.rutgers.edu> Sent: Wednesday, December 2, 2020 8:51 AM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] question about dihedral angles [EXTERNAL SENDER - PROCEED CAUTIOUSLY] On Wed, Dec 02, 2020, Karl Kirschner wrote: > >impose mymolecule {7} { {C1 C2 C3 C4 120.0} } One point is this: the command above doesn't specific which atoms are to be *moved* in order to make the dihderal be 120 degrees. Should the program move C4 (and atoms bonded to it), or move C1 (and atoms bonded to it)? Or do something else? This may not be important in some workflows, but can be key in others. The pyMol example has the same problem. Of course, its documentation may be better in explaining what choices are made. These sorts of manipulations are a natural for NAB (aka "molecular awk"), but it has its own learning curve and documentation deficiencies. ....dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 15 Date: Wed, 2 Dec 2020 14:03:51 +0000 From: Gordon Richard Chalmers <gordoncs.uga.edu> Subject: Re: [AMBER] question about dihedral angles To: AMBER Mailing List <amber.ambermd.org> Message-ID: <DM5PR02MB2715D20E3D3F3E02D24DE6F2DCF30.DM5PR02MB2715.namprd02.prod.outlook. com> Content-Type: text/plain; charset="us-ascii" Thank you for the help in this. In a protein the phi and psi angles require 2 adjacent residues. Calculating these angles and rotating is fairly easy. It is a matter of what is rotated to agree to a PDB model starting from a linear backbone model. I will be working the angle rotations further in tleap today, a little delayed at the moment. In principle, you should rotate the entire peptide chain after or before the ith residue as these are bonded in %% phi C(i-1)-N-CA-C %% psi N-CA-C-N(i+1) The actual rotation angle about the intermediary N-CA or CA-C axis should be the dihedral angle geometrically. Maybe my own Matlab algorithms aren't correct yet, but I have checked this many times. I will try to use tleap or cpptraj instead as a check. Gordon Chalmers Department of Computer Science Complex Carbohydrate Research Center University of Georgia ________________________________ From: David A Case <david.case.rutgers.edu> Sent: Wednesday, December 2, 2020 8:51 AM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] question about dihedral angles [EXTERNAL SENDER - PROCEED CAUTIOUSLY] On Wed, Dec 02, 2020, Karl Kirschner wrote: > >impose mymolecule {7} { {C1 C2 C3 C4 120.0} } One point is this: the command above doesn't specific which atoms are to be *moved* in order to make the dihderal be 120 degrees. Should the program move C4 (and atoms bonded to it), or move C1 (and atoms bonded to it)? Or do something else? This may not be important in some workflows, but can be key in others. The pyMol example has the same problem. Of course, its documentation may be better in explaining what choices are made. These sorts of manipulations are a natural for NAB (aka "molecular awk"), but it has its own learning curve and documentation deficiencies. ....dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 16 Date: Wed, 2 Dec 2020 14:10:11 +0000 From: Gordon Richard Chalmers <gordoncs.uga.edu> Subject: Re: [AMBER] question about dihedral angles To: AMBER Mailing List <amber.ambermd.org> Message-ID: <DM5PR02MB271576BCB52CD93FA422316FDCF30.DM5PR02MB2715.namprd02.prod.outlook. com> Content-Type: text/plain; charset="us-ascii" Another point: it is possible to do a search of the peptide bond angles to find what is being rotated in order to agree with a PDB model, but this sort of defeats the purpose of simple linear rotations. TBD. Gordon Chalmers ________________________________ From: Gordon Richard Chalmers <gordoncs.uga.edu> Sent: Wednesday, December 2, 2020 9:03 AM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] question about dihedral angles Thank you for the help in this. In a protein the phi and psi angles require 2 adjacent residues. Calculating these angles and rotating is fairly easy. It is a matter of what is rotated to agree to a PDB model starting from a linear backbone model. I will be working the angle rotations further in tleap today, a little delayed at the moment. In principle, you should rotate the entire peptide chain after or before the ith residue as these are bonded in %% phi C(i-1)-N-CA-C %% psi N-CA-C-N(i+1) The actual rotation angle about the intermediary N-CA or CA-C axis should be the dihedral angle geometrically. Maybe my own Matlab algorithms aren't correct yet, but I have checked this many times. I will try to use tleap or cpptraj instead as a check. Gordon Chalmers Department of Computer Science Complex Carbohydrate Research Center University of Georgia ________________________________ From: David A Case <david.case.rutgers.edu> Sent: Wednesday, December 2, 2020 8:51 AM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] question about dihedral angles [EXTERNAL SENDER - PROCEED CAUTIOUSLY] On Wed, Dec 02, 2020, Karl Kirschner wrote: > >impose mymolecule {7} { {C1 C2 C3 C4 120.0} } One point is this: the command above doesn't specific which atoms are to be *moved* in order to make the dihderal be 120 degrees. Should the program move C4 (and atoms bonded to it), or move C1 (and atoms bonded to it)? Or do something else? This may not be important in some workflows, but can be key in others. The pyMol example has the same problem. Of course, its documentation may be better in explaining what choices are made. These sorts of manipulations are a natural for NAB (aka "molecular awk"), but it has its own learning curve and documentation deficiencies. ....dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 17 Date: Wed, 2 Dec 2020 11:50:58 -0500 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] question about dihedral angles To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOZ6fau_S4hV-7f=bd-8PLdS2AN4864spumxQ+4f6d=FVg.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi, The command for calculating dihedral angles in cpptraj is 'dihedral'. The command for rotating atoms around a dihedral is 'rotatedihedral'. Both are documented in the manual. The convention in cpptraj is for all atoms connected to the greater atom index to move; those connected to the lower atom index are fixed. Cpptraj does the rotation in Cartesian space - I think tleap may do it via internal coordinates but I'm not sure about that. -Dan On Wed, Dec 2, 2020 at 9:04 AM Gordon Richard Chalmers <gordoncs.uga.edu> wrote: > > > Thank you for the help in this. > > In a protein the phi and psi angles require 2 adjacent > residues. Calculating these angles and rotating is > fairly easy. It is a matter of what is rotated to agree > to a PDB model starting from a linear backbone model. > > I will be working the angle rotations further in tleap today, > a little delayed at the moment. > > In principle, you should rotate the entire peptide chain > after or before the ith residue as these are bonded in > > %% phi C(i-1)-N-CA-C > %% psi N-CA-C-N(i+1) > > The actual rotation angle about the intermediary N-CA > or CA-C axis should be the dihedral angle geometrically. > > Maybe my own Matlab algorithms aren't correct yet, but > I have checked this many times. I will try to use tleap or > cpptraj instead as a check. > > Gordon Chalmers > Department of Computer Science > Complex Carbohydrate Research Center > University of Georgia > ________________________________ > From: David A Case <david.case.rutgers.edu> > Sent: Wednesday, December 2, 2020 8:51 AM > To: AMBER Mailing List <amber.ambermd.org> > Subject: Re: [AMBER] question about dihedral angles > > [EXTERNAL SENDER - PROCEED CAUTIOUSLY] > > > On Wed, Dec 02, 2020, Karl Kirschner wrote: > > > >impose mymolecule {7} { {C1 C2 C3 C4 120.0} } > > One point is this: the command above doesn't specific which atoms are to > be *moved* in order to make the dihderal be 120 degrees. Should the > program move C4 (and atoms bonded to it), or move C1 (and atoms bonded > to it)? Or do something else? This may not be important in some > workflows, but can be key in others. > > The pyMol example has the same problem. Of course, its > documentation may be better in explaining what choices are made. > > These sorts of manipulations are a natural for NAB (aka "molecular > awk"), but it has its own learning curve and documentation deficiencies. > > ....dac > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber End of AMBER Digest, Vol 3201, Issue 1 ************************************** -- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Dec 04 2020 - 10:00:02 PST