[gmx-users] Broken bonds between peptide and capped terminals when solvated

Hi all, I have a capped peptide and when i solvate the system with water and visualize it in vmd, the bonds between the peptide and corresponding capped N and C terminal groups is not seen (or) broken. Whereas before solvating the system, the bonds between the peptide and corresponding capped N

[gmx-users] Unusual bond between residues which are capped

Hi all, I have a peptide which is capped on the N-terminal and C-terminal with acetyl and N-methyl groups. But when i view this in vmd, i get the following error as: Warning) Unusual bond between residues: 1 (none) and 2 (protein) Warning) Unusual bond between residues: 8 (protein) and 9 (none)

Re: [gmx-users] Tilt- angle Distribution

Have a read through the list of scripts included with GROMACS, always a good thing to do to see what is possible, you might spot something you hadn't thought of using: http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#commands-by-name gmx helixorient might be what you are

Re: [gmx-users] index file for special residues

"|" = or What you want is "&" = and aptamer | r special = aptamer aptamer & r special = special 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

Re: [gmx-users] Use of index file generated by gmx select

gmx scripts have the -n switch, which you can use to pass an index.ndx file to, then control which particles the script then applies the analysis too. http://manual.gromacs.org/documentation/current/onlinehelp/gmx-velacc.html#options

Re: [gmx-users] non-water solvent + gmx solvate

Hi Kevin, I'm using 2018.2 -- had to roll 2019 back because it segfaults on a certain simulation setup (I posted earlier about that, got no responses). Kind of a disappointing situation... I guess I will use packmol or just script it with insert-molecules. Alex On 5/26/2019 8:31 AM, Kevin

Re: [gmx-users] non-water solvent + gmx solvate

Hi, Which version are you using? As of 2019 gmx solvate should support nonwater solvents and topology updating. If it’s not working with 2019, can you open up an issue on redmine.gromacs.org and upload your use files? I can take a look. Thanks, Kevin > On May 26, 2019, at 9:44 AM, Jones de

Re: [gmx-users] non-water solvent + gmx solvate

Hi. Have you tried the packmol software? Good luck, Jones -- Jones de Andrade (jdandr...@iq.ufrgs.br) DFQ/IQ/UFRGS Lattes: http://lattes.cnpq.br/6675936210583999 Orcid: https://orcid.org/-0003-3429-8119 Enviado pelo K-9 mail Em 26 de maio de 2019 04:22:58 BRT, Alex escreveu: >Hi all, >

Re: [gmx-users] error of missing atoms due to an incorrectness in the .hdb file

Thank you Justin, I worked more on the format of hydrogen names and I don't see those errors anymore. However, the only error I now see is: "Atom H5'1 not found in rtp database in residue FAD, it looks a bit like H01". Which is weird, because there is no atom named H5'1 anywhere! Not in the pdb,

[gmx-users] Tilt- angle Distribution

dear users, Is there any module in gromacs to calculate the tilt angle distribution? -- 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

[gmx-users] umberlla sampling of protein ligand complex

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said:

Re: [gmx-users] Regarding Simulation

Hi, That is normal, Gromacs writes checkpoint in case of your simulation crash (electric power issue or time limit) so that Gromacs can continue the simulation from the checkpoint. By default, 15min is the time interval of writing checkpoint On Sun, May 26, 2019 at 8:16 AM Omkar Singh wrote: >

[gmx-users] index file for special residues

Dear all, I am going to generate index file for special residues in my aptamer, I use the command " make_ndx -f *.gro -o index.ndx and then select group as DNA and Special residue as fallow ">1|r 4 5 7 36. The index file for whole aptamer and special residue is similar, I would be appreciate

[gmx-users] non-water solvent + gmx solvate

Hi all, I have a custom model for acetonitrile, which works fine when filling up a box using insert-molecules. When trying to use gmx solvate starting from a non-empty box, the utility displays a promising "Generating solvent configuration" and proceeds into nothingness with 100% CPU load.

[gmx-users] Use of index file generated by gmx select

Hello, I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps interval. I am using gmx select to generate a index.ndx of 25 index for water molecules within 0.5nm of the protein. I want to know how to use this index.ndx file for my calculation - For example: a) If I want to

[gmx-users] Regarding Simulation

Hello gromacs users, I am doing protein-water simulation with calculating velocity. I am getting thins kind of checkpoint files, Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.92508e+031.15716e+036.91130e+02 -1.22494e+02

[gmx-users] LIE free energy coefficients

Hello I want to compute binding free energy of an amino-acid interaction with one zinc metal ion. What coefficients must be used when I choose the peptide or the amino acid as ligand? Regards, Mohsen -- Gromacs Users mailing list * Please search the archive at