Re: [gmx-users] Selection of residues in one of the chains of heterodimer

Hi! The gro file lost the data about the chains and treated the entire heterodimer as one chain. Anyway, problem solved! I checked the atom numbers from the gro file and selected those in VMD. A bit tedious, but worked! Thank you and regards, Raag -- Gromacs Users mailing list * Please search

Re: [gmx-users] Temperature in CG production runs

On 10/29/18 6:34 AM, Yasser Almeida Hernández wrote: Dear all, I am performing CG simulations (Martini) of a membrane protein in an heterogeneous model bilayer with several lipids, resembling the inner membrane from E. coli. Looking in the literature, I have seen that the temperature for

Re: [gmx-users] Error of CgenFF convert to itp

On 10/28/18 11:04 PM, Mijiddorj B wrote: I would like to generate parameters for small molecule using CGenFF. I generated str file using cgenFF. However, I could not convert to itp file using cgenff_charmm2gmx.py because of following error: Please advice me. NOTE2: Please be sure to use the

Re: [gmx-users] gro to itp file

On 10/27/18 2:53 AM, Anubha Agrawal wrote: Yes @soumadwip sir, you are right but my residue entry in .rtp file lacks the information of dihedral and angles so I won't get the files supposed to obtain from pdb2gmx. I want to know if there is an option to self-consistently generate angles,

Re: [gmx-users] gro to itp file

On 10/26/18 10:13 AM, Anubha Agrawal wrote: Hello gmx users, Please ignore my previous post. My query is following- I've prepared a coordinate file in .gro format using pdb2gmx. I obtained the pdb from openbabel online server and used it for pdb2gmx command. Further, I've identified CHARMM36

Re: [gmx-users] No default Angle types

On 10/25/18 6:37 AM, antonia vyrkou wrote: Hello, After running gmx grompp I get multiple errors like the following: ERROR 568 [file topol_Other_chain_D2.itp, line 499]: No default Angle types This line corresponds to the angle (using angletypes) HN1 NN1 HN1 This angle (and

Re: [gmx-users] Adding residue to .rtp file

On 10/24/18 2:46 PM, Raji wrote: Thank you for your reply. I have few more questions 1. Yes, command pdb2gmx continued and generated the topology. The warning is about 74 atoms which are from the new added rtp entry. I just want to understand more about the warning. I dont find any related

Re: [gmx-users] Selection of residues in one of the chains of heterodimer

So, what is the difference between the 2 PDB files? What information was in the original PDB file, that was then lost when converted to the GRO file, then was not recovered when that was converted to a PDB? Load the files with a text editor, you will see what information is contained in each and

Re: [gmx-users] acpype

Are you running python3? what python -V or python3 -V outputs? Alan On Mon, 29 Oct 2018 at 13:25, neelam wafa wrote: > Hi > Thanks for your help. I have resolved that problem but got another one . > when I run the command > > ../acpype.py -i FFF.pdb > > I get this error. > File

Re: [gmx-users] gmx kill computer?

On Tue, Oct 23, 2018 at 4:04 PM Wahab Mirco < mirco.wa...@chemie.tu-freiberg.de> wrote: > On 23.10.2018 15:12, Michael Brunsteiner wrote: > > the computers are NOT overclocked, cooling works, cpu temperatures are > well below max. > > as stated above something like this happened three times, each

Re: [gmx-users] And Ryzen 8 core/16 thread use

Sure, if you use the recent releases with PME offload, you might even be able to drive two GPUs with it. I also do not know of cooling issues, is there anything specific you are referring to? -- Szilárd On Thu, Oct 25, 2018 at 5:27 PM paul buscemi wrote: > > Dear Users, > > Does anyone have

Re: [gmx-users] acpype

Hi Thanks for your help. I have resolved that problem but got another one . when I run the command ../acpype.py -i FFF.pdb I get this error. File "../acpype.py", line 561 def __init__(self) -> None: ^ SyntaxError: invalid syntax can you please help me out of the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 71

Please install anaconda3 first. Delete your previous anconda2 from your home. Simply download install script from anaconda website. and the run it using bash Anaconda--- Then let me know Thanks Bhupendra On Mon, Oct 29, 2018 at 4:22 PM Farial Tavakoli wrote: > Hi Bhupendra > > yes i am on

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 71

Hi Bhupendra yes i am on lone now. Farial On Mon, Oct 29, 2018 at 2:11 PM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide

[gmx-users] Temperature in CG production runs

Dear all, I am performing CG simulations (Martini) of a membrane protein in an heterogeneous model bilayer with several lipids, resembling the inner membrane from E. coli. Looking in the literature, I have seen that the temperature for production runs range from 300-330K, which are a big

[gmx-users] Selection of residues in one of the chains of heterodimer

Hi! I simulated a heterodimer and converted the md.gro file into a pdb file. This pdb file I visualised in vmd. I wish to select residues (first 50, then next 50 and so on), so that I can correlate the structure with the graphs obtained by structure analysis. If I give the command resid 1 to 50

[gmx-users] Place a gap in y-axis

Hi! This is not really a gromacs question, but I was wondering if you could help, please! I have a multiple line plot with a major difference between one of the plots and the rest. Hence, I need to insert a gap in the y axis. I usually use grace to plot the graphs generated by gromacs, but I’m

Re: [gmx-users] acpype and conda

Hi Farial, Are you online now? Bhupendra On Mon, Oct 29, 2018 at 12:10 PM Farial Tavakoli wrote: > Dear Bhupendra > > Thanks for your reply > > I am in /Downloads/acpype-master/acpype/scripts path and type only acpype > -h or acpype.py -h , but face with this error: > acpype: command not

[gmx-users] acpype and conda

Dear Bhupendra Thanks for your reply I am in /Downloads/acpype-master/acpype/scripts path and type only acpype -h or acpype.py -h , but face with this error: acpype: command not found I can run acpype only when type python command before it. In addition, I installed