Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul) (Sadaf Rani)
Thank you very much, Justin, for your valuable feedback. Regards. Sadaf -- 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] Lincs warning in free energy calculation (FAISAL NABI)
Dear Gromacs users I am using amber99sb-ildn.ff force field for protein and I used GAFF for ligand parameterization. I tried different options e.g using constraint =all bonds as well as h-bonds. Reducing the time step to 1 fs but still, I could not solve the problem and get lincs warning production run as below:- Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035343, max 2.112628 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.02.2392 0.1552 0.1080 3770 3771 90.00.1045 0.1696 0.1090 3770 3772 90.02.9369 0.1212 0.1090 3770 3773 90.00.1043 0.3393 0.1090 Wrote pdb files with previous and current coordinates Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035038, max 2.096736 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.02.2392 0.1540 0.1080 3770 3771 90.00.1045 0.1689 0.1090 3770 3772 90.02.9369 0.1198 0.1090 3770 3773 90.00.1043 0.3375 0.1090 I would really appreciate your help in fixing this problem I am facing since long. Thanks. Sadaf -- 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] Lazaro Andres Monteserin Castanedo shared "dPCA" with you
Hi Nikhil, Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited you to edit the folder " dPCA " on Dropbox. Lazaro Andres said: "Dear Dr. Lemkul I used the following protocol to generate the (.xpm) filesI followed the protocol in gromacs website to do dihedral Principal Component Analysis1) Created an index file (dangle.ndx) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before.2) Then I extracted the sincos of the angles in the dangle.ndx from my MD in the file (dangle.trr) with the following commandgmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral(I had 21 angles so it used 14 sincos to represent the angles)3) Then I generated an index file (covar.ndx) with a list of numbers from 1 to 14 for trjconv.4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysisgmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 11 was the time in ps for the last frame of the simulation.5) I runned covargmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectorsgmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg7) Then I got the projection in 3D of the free energy landscapegmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpmI would appreciate any feedbackThank you in advance Dr. LemkulKindly,Lazaro" Go to folder[1] Enjoy! The Dropbox team [1]: https://www.dropbox.com/l/scl/AACmJPduzqbNRmC7scaafSZ0pkU9B-KtLvo -- 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] dPCA - Compartido desde Dropbox
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/t0atsemijjmfo6m/AADGwMfvaSGaJTUOlCu_Gazla?dl=0 I would appreciate any feedback Thank you in advance Dr. Lemkul Kindly, Lazaro -- 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] about how to create angle.index with specific angles
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0 I would appreciate any feedback Thank you in advance Dr. Lemkul Kindly, Lazaro On Sat, May 2, 2020 at 8:47 AM Justin Lemkul wrote: > > > On 4/30/20 2:07 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. > > > > Now I am having issues opening the (.xpm) files generated that contain > for > > example the gibbs energy landscape on the two first eigenvectors of the > > dPCA. > > > > If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o > gibbs-1_2.eps" > > it write this error: "Input error or input inconsistency: > > Invalid XPixMap" > > > > Do you know if I am missing something here? Do I have to install > something > > in my OS to be able to see .xpm images? > > The error is coming from xpm2ps which means there's something wrong with > the .xpm file itself but without seeing how you generated it (exact > command and description of how you prepared the input data file) and > perhaps the .xpm file itself (uploaded somewhere), it's impossible to > comment further. > > -Justin > > > Thanks in advance, > > > > Lazaro > > > > On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: > > > >> > >> On 4/29/20 7:11 PM, lazaro monteserin wrote: > >>> Dear Dr. Lemkul it could be possible use that angle.index with the > >> selected > >>> dihedrals written by hand as index file for gmx angle for dihedral > >>> Principal Component Analysis? > >> You can create index groups however you like for whatever analysis you > >> want to perform. > >> > >> -Justin > >> > >>>Kindly, > >>> Lazaro > >>> > >>> On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > >>> > On 4/29/20 5:01 PM, lazaro monteserin wrote: > > Dear gromacs users, > > > > Is there any way to tell gmx mk_angndx to create the index file with > > dihedral angles from a (.tpr) for specific atom numbers (atom level, > >> e.g > 1, > > 2, 3) from my molecule? > mk_angndx is designed for distributions of similar angles (e.g. > evaluating force field sampling). If you want to compute specific > angles, use make_ndx or simply write the index groups by hand. > > -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 > >>
[gmx-users] Failed make check
Hello all, I was trying to install GROMACS 2020.2 and encountered a failed test at make check (#43, mdrun). I pasted what I think is the pertinent snippet below and the full output is in the link: https://www.dropbox.com/s/nfq6yojjdslhxur/make_check.log?dl=0 The cmake incovation was: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on I have been using GROMACS 2020 on the machine with various GTX GPUs without issues. For what it's worth, when I re-ran make check for that version, it passed. Many thanks for your help in advance, Gregory [--] 1 test from OriresTest [ RUN ] OriresTest.OriresCanRun NOTE 1 [file /home/e5-1650/Downloads/gromacs-2020.2/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to -949742347 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 518.00 NOTE 2 [file /home/e5-1650/Downloads/gromacs-2020.2/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Reading file /home/e5-1650/Downloads/gromacs-2020.2/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020 (single precision) Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. --- Program: mdrun-test, version 2020 Source file: src/gromacs/listed_forces/orires.cpp (line 127) Fatal error: Found 10 copies of a molecule with orientation restrains while the current code only supports a single copy. If you want to ensemble average, run multiple copies of the system using the multi-sim feature of mdrun. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- 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] Redmine posting forbidden?
On 5/2/20 12:13 PM, Eugene Radchenko wrote: Hello, I wanted to report a bug using the Redmine site. Unfortunately, even after registering, the option to submit an issue is missing from the Issues page (where I expected it). While the “File a new issue” link from the main page to https://redmine.gromacs.org/projects/gromacs/issues/new results in Error 403 “You are not authorized to access this page”. Am I doing something wrong? We use GitLab now: https://gitlab.com/gromacs -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.
[gmx-users] Redmine posting forbidden?
Hello, I wanted to report a bug using the Redmine site. Unfortunately, even after registering, the option to submit an issue is missing from the Issues page (where I expected it). While the “File a new issue” link from the main page to https://redmine.gromacs.org/projects/gromacs/issues/new results in Error 403 “You are not authorized to access this page”. Am I doing something wrong? Thank you Eugene -- 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] disulfide bridges
Oh thank you so much, I did not know it was a reference value. Given a range of values might exist in one system I'm guessing minimization would be the only way to deal with such a situation. Best, Miro On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote: > > > On 5/2/20 6:54 AM, Miro Astore wrote: > > Hi all, > > > > I'm trying to make a protein with a fair few disulfide bridges and I > > couldn't get it to work. I chose -ss yes and increased the minimum > distance > > in specbonds.dat but it doesn't seem to want to let me see all possible > > pariings. > > specbond.dat does not set minimum distances. It sets a reference value, > and a bond is only assigned if the distance in the coordinate file is > within 10% of that reference. So if you were, for example, to increase > the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the > disulfides that should be formed because the new reference range is 0.27 > - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a > disulfide linkage. > > > Any way I can nudge it in the right direction without performing a > > minimisation with restraints? > > Depends on the range of distances in your structure, but this is often > what you have to do. > > -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. > -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] Warning: Short Bond pdb2gmx (Justin Lemkul)
On 5/2/20 8:21 AM, Sadaf Rani wrote: Dear Justin I want to get the equilibrium value for bond, angle and dihedral restraints to use in free energy calculation as mentioned in:- https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467 Looking forward to your kind suggestions, please. You can compute all geometric properties from a simulation using gmx distance, gmx angle, etc. -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] Warning: Short Bond pdb2gmx (Justin Lemkul)
Dear Justin I want to get the equilibrium value for bond, angle and dihedral restraints to use in free energy calculation as mentioned in:- https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467 Looking forward to your kind suggestions, please. Thanks. Sadaf -- 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] disulfide bridges
On 5/2/20 6:54 AM, Miro Astore wrote: Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. specbond.dat does not set minimum distances. It sets a reference value, and a bond is only assigned if the distance in the coordinate file is within 10% of that reference. So if you were, for example, to increase the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the disulfides that should be formed because the new reference range is 0.27 - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a disulfide linkage. Any way I can nudge it in the right direction without performing a minimisation with restraints? Depends on the range of distances in your structure, but this is often what you have to do. -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] Warning: Short Bond pdb2gmx
On 5/1/20 2:41 PM, Sadaf Rani wrote: Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restraints. but when I do gmx pdb2gmx I get following warning:- Warning: Short Bond (9-10 = 0.042416 nm) Warning: Short Bond (9-11 = 0.0463433 nm) Warning: Short Bond (9-12 = 0.0452425 nm) Warning: Short Bond (13-14 = 0.0407501 nm) Warning: Short Bond (13-15 = 0.0425715 nm) Warning: Short Bond (13-16 = 0.0421154 nm) Warning: Short Bond (65-66 = 0.0418464 nm) Warning: Short Bond (65-67 = 0.0454554 nm) Warning: Short Bond (65-68 = 0.0438005 nm) Warning: Short Bond (103-105 = 0.0498706 nm) Warning: Short Bond (103-106 = 0.0482166 nm) Warning: Short Bond (161-162 = 0.0384303 nm) Warning: Short Bond (161-163 = 0.0395632 nm) Warning: Short Bond (161-164 = 0.0404804 nm) Warning: Short Bond (178-179 = 0.0379231 nm) Warning: Short Bond (178-180 = 0.0350074 nm) Warning: Short Bond (178-181 = 0.0367544 nm) Warning: Short Bond (195-197 = 0.0491068 nm) Warning: Short Bond (240-241 = 0.0410752 nm) Warning: Short Bond (240-242 = 0.0400188 nm) Warning: Short Bond (240-243 = 0.0389276 nm) Warning: Short Bond (244-245 = 0.0395354 nm) Warning: Short Bond (244-246 = 0.0394185 nm) Warning: Short Bond (244-247 = 0.0411173 nm) Warning: Short Bond (254-255 = 0.0496385 nm) Warning: Short Bond (254-256 = 0.0490917 nm) Warning: Short Bond (254-257 = 0.0487225 nm) Warning: Short Bond (320-321 = 0.0389006 nm) Warning: Short Bond (320-322 = 0.0354672 nm) Warning: Short Bond (320-323 = 0.0318275 nm) Warning: Short Bond (332-333 = 0.044048 nm) Warning: Short Bond (332-334 = 0.0431301 nm) Warning: Short Bond (332-335 = 0.0443143 nm) Warning: Short Bond (339-340 = 0.0436942 nm) Warning: Short Bond (339-341 = 0.044572 nm) Warning: Short Bond (339-342 = 0.0438389 nm) Warning: Short Bond (386-387 = 0.0485982 nm) Warning: Short Bond (386-388 = 0.0493432 nm) Warning: Short Bond (400-401 = 0.0365161 nm) Warning: Short Bond (400-402 = 0.043 nm) Warning: Short Bond (400-403 = 0.038517 nm) Warning: Short Bond (552-553 = 0.0489085 nm) Warning: Short Bond (552-554 = 0.0483887 nm) Warning: Short Bond (552-555 = 0.0498913 nm) Warning: Short Bond (556-557 = 0.0345456 nm) Warning: Short Bond (556-558 = 0.0396005 nm) Warning: Short Bond (556-559 = 0.0370519 nm) Warning: Short Bond (575-576 = 0.0458407 nm) Warning: Short Bond (575-577 = 0.0455252 nm) Warning: Short Bond (575-578 = 0.0448519 nm) Warning: Short Bond (664-665 = 0.0423401 nm) Warning: Short Bond (664-666 = 0.0390075 nm) Warning: Short Bond (664-667 = 0.0406177 nm) Warning: Short Bond (671-672 = 0.0369435 nm) Warning: Short Bond (671-673 = 0.0354056 nm) Warning: Short Bond (671-674 = 0.0373171 nm) Warning: Short Bond (725-726 = 0.0389842 nm) Warning: Short Bond (725-727 = 0.0393952 nm) I understand that the average structure is not necessarily anything physically meaningful but how I assume that it can give the equilibrium values to set the restraints. What kind of restraints are you trying to set? I need your help to figure out this warning, please. The warning indicates what you've already read about average structures - they are physically nonsensical. You can't start a simulation from an average structure because it is totally distorted and therefore of essentially no use for almost anything. -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] PBC after energy minimization
On 5/1/20 9:29 AM, John Whittaker wrote: Hi Mohamed, Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have .xtc file to use it as I do at the end. How can I solve this problem after the energy minimization ? You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. "Trajectories" from energy minimization are generally unreadable as the interval of saved frames is uneven. During EM, a frame is only written when the energy goes down, which is not necessarily every possible frame. I also seem to recall that there is never XTC output from EM, even if requested, because it's rather pointless. Maybe that has changed. -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] about how to create angle.index with specific angles
On 4/30/20 2:07 PM, lazaro monteserin wrote: Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps" it write this error: "Input error or input inconsistency: Invalid XPixMap" Do you know if I am missing something here? Do I have to install something in my OS to be able to see .xpm images? The error is coming from xpm2ps which means there's something wrong with the .xpm file itself but without seeing how you generated it (exact command and description of how you prepared the input data file) and perhaps the .xpm file itself (uploaded somewhere), it's impossible to comment further. -Justin Thanks in advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: On 4/29/20 7:11 PM, lazaro monteserin wrote: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? You can create index groups however you like for whatever analysis you want to perform. -Justin Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -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. -- == 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.
[gmx-users] disulfide bridges
Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. Any way I can nudge it in the right direction without performing a minimisation with restraints? Best, Miro -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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.
