Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul) (Sadaf Rani)

2020-05-02 Thread 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

Re: [gmx-users] Lincs warning in free energy calculation (FAISAL NABI)

2020-05-02 Thread Sadaf Rani
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

[gmx-users] Lazaro Andres Monteserin Castanedo shared "dPCA" with you

2020-05-02 Thread Lazaro Andres Monteserin Castanedo (via Dropbox)
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

[gmx-users] dPCA - Compartido desde Dropbox

2020-05-02 Thread lazaro monteserin
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

Re: [gmx-users] about how to create angle.index with specific angles

2020-05-02 Thread lazaro monteserin
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

[gmx-users] Failed make check

2020-05-02 Thread Gregory Man Kai Poon
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 ..

Re: [gmx-users] Redmine posting forbidden?

2020-05-02 Thread Justin Lemkul
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

[gmx-users] Redmine posting forbidden?

2020-05-02 Thread Eugene Radchenko
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

Re: [gmx-users] disulfide bridges

2020-05-02 Thread Miro Astore
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

Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul)

2020-05-02 Thread 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

Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul)

2020-05-02 Thread Sadaf Rani
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

Re: [gmx-users] disulfide bridges

2020-05-02 Thread Justin Lemkul
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

Re: [gmx-users] Warning: Short Bond pdb2gmx

2020-05-02 Thread Justin Lemkul
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

Re: [gmx-users] PBC after energy minimization

2020-05-02 Thread Justin Lemkul
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

Re: [gmx-users] about how to create angle.index with specific angles

2020-05-02 Thread Justin Lemkul
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-users] disulfide bridges

2020-05-02 Thread Miro Astore
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