Re: [gmx-users] acpype

We are working on it now. I can't tell you exactly because we need several tests. It's a complete new version re-written from scratch. I'm really sorry for the inconvenience but we hope to bring it back in a month or two. Alan On Wed, 24 Oct 2018 at 16:58, neelam wafa wrote: > Hi alan > > Can

Re: [gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

Haven't tried it, but seems to me you generate a .tpr file with the protein orientated correctly within the box, then use trjconv -fit Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville

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

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 information? 2. What is the significance

Re: [gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

Hi Stéphane I am interested in the lipid density around the protein, so I only choose the lipid bilayer to plot 2D density map. Regarding the coordinates, I need to remove the pbc box effect by 'pbc mol' of trajconv function so that the protein will be complete, or in Amber, cpptraj with

[gmx-users] Simulated tempering

Hi all, I am attempting to do simulated tempering on GROMACS 2016.3.  In my preliminary googling, I have found several questions from different people on the procedure in the past few years but unfortunately without response.  I have read up on the literature on the few papers that described

Re: [gmx-users] acpype

Hi alan Can you please tell how long will it take for the online acpype server to be available? Regards Neelam wafa On Wed, 24 Oct 2018, 6:23 pm Alan, wrote: > Indeed, it's mostly Luciano spearheading these new things. Hopefully, we > will have more things to show eventually. > > Alan > > On

[gmx-users] acpype

Dear Justin I installed acpype on the ubuntu but didnt install Antechamber and openbable . Now I am trying to convert the AMBER parameters format (obtained from  http://sites.pharmacy.manchester.ac.uk/bryce/amber  ) to the one that gromacs is compatible with in the .rtp files. I pasted acpype.py

Re: [gmx-users] acpype

Indeed, it's mostly Luciano spearheading these new things. Hopefully, we will have more things to show eventually. Alan On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar < bhupendra.dandekar...@gmail.com> wrote: > I actually got lot of help from Luciano Kagami about installation and usage > of

Re: [gmx-users] acpype

I actually got lot of help from Luciano Kagami about installation and usage of acpype and ligro. Thanks to both of you. Bhupendra On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar < bhupendra.dandekar...@gmail.com> wrote: > Thanks to you also sir. > Your work is really appreciated and is

Re: [gmx-users] acpype

Thanks to you also sir. Your work is really appreciated and is really helpful. Bhupendra On Wed, Oct 24, 2018 at 3:59 PM Alan wrote: > Thanks Bhupendra, indeed we have this option, which is experimental, but > I'm glad to see some are already using it and it seems to be working. > > Alan > >

Re: [gmx-users] gmx kill computer?

On 24.10.2018 11:07, Michael Brunsteiner wrote: > Harry and Mirco!I've got 700W Thermaltake PSUs here ... according to several > web-sites thatcalculate the expected power consumption for a given set of > components, and alsoin our experience this should be more than enough ...Can > it be that,

Re: [gmx-users] nvcc fatal: 'avx512f': expected a number

Hi, On Wed, Oct 24, 2018 at 11:50 AM Ehsan Moravveji wrote: > Dear Mark, > > Sincere thanks for your swift reply, and apologies for the duplicate > message; I realized that my original message had no subject, so, I thought > it is more proper to send the message with a meaningful topic; > OK

Re: [gmx-users] acpype

Thanks Bhupendra, indeed we have this option, which is experimental, but I'm glad to see some are already using it and it seems to be working. Alan On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar < bhupendra.dandekar...@gmail.com> wrote: > Dear Farial, > > Use this command to install acpype

Re: [gmx-users] acpype

Dear Farial, Use this command to install acpype and antechamber using conda: conda install -c acpype -c openbabel -c ambermd and then you can check and call acpype, antechamber like this from your terminal: acpype -h antechamber -h then you can generate ligand topology using this command:

Re: [gmx-users] nvcc fatal: 'avx512f': expected a number

Dear Mark, Sincere thanks for your swift reply, and apologies for the duplicate message; I realized that my original message had no subject, so, I thought it is more proper to send the message with a meaningful topic; Regarding your comment, I am building GROMACS from source, and without

[gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

Hello All, I have basic questions regarding the procedure to generate an new xtc where a membrane protein inserted a detergent micelle is properly oriented for the computation of 2D density Map. Indeed for this calculation I need to have the protein-surfactant complex properly oriented along

Re: [gmx-users] acpype

Latest acpype is here: https://github.com/alanwilter/acpype Mind that it's *only* Python 3 compatible now. Run something like this, at first, to be sure: _full_to_your_python3 _full_path_to_acpype -d -i ... You need Antechamber (from Amber) if you want to generate topologies. Only if

[gmx-users] gmx kill computer?

Hi, Thanks for you replies, Harry and Mirco!I've got 700W Thermaltake PSUs here ... according to several web-sites thatcalculate the expected power consumption for a given set of components, and alsoin our experience this should be more than enough ...Can it be that, as Mirco suggested, the

Re: [gmx-users] nvcc fatal: 'avx512f': expected a number

Hi, You sent this email yesterday. Please be a little more patient. Unfortunately, I have no idea how EasyBuild works, and suspect that the problem lies in the way it is wrapping arguments that then get passed to nvcc. If you can reproduce this issue with a simple call to cmake with minimal

[gmx-users] acpype

Dear GMX useres I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter database (Bryce Group: Computational Biophysics and Drug Design - University of Manchester) to the format that GROMACS is compatible with in .rtp

[gmx-users] acpype

Dear GMX useres I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter database (Bryce Group: Computational Biophysics and Drug Design - University of Manchester) to the format that GROMACS is compatible with in .rtp files. so referred to GROMACS tutorial protein-ligand

[gmx-users] nvcc fatal: 'avx512f': expected a number

Dear GMX users, I would like to share a difficulty installing GROMACS/2018.3 with you, and kindly ask for your wisdom. I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes equipped with 4 x P100 Nvidia devices. Below is the cmake configuration that I use, followed by the

Re: [gmx-users] Location of latest version of Acpype

Please, see here https://github.com/alanwilter/acpype And many thanks for using ACPYPE! Alan On Tue, 23 Oct 2018 at 21:02, Matthew Fisher wrote: > Dear all, > > > I'm currently trying to locate the latest version of acpype and have been > unable to find a working link to the script/installer.

Re: [gmx-users] missing atoms in residues

Use whatif server to complete ur structure On Wed, Oct 24, 2018, 11:57 AM Rahma Dahmani wrote: > Hi everyone, > I have one question: Is it possible to add missing atoms in residues using > gromacs ? ( PS. i already tried pdb2gmx but it didn't work out) > missing atoms are : > GLU A 117CB

Re: [gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

Hello Stéphane, I happened to use densmap and xpm these days for my ion channel. Here is an example that you can play with for your system. gmx densmap -f md.xtc -s md.tpr -n index.ndx -aver z -bin 0.05 -dmin 0 -dmax 20 -unit nm-2 -o md.xpm ( later choose the group you are interested in)

[gmx-users] missing atoms in residues

Hi everyone, I have one question: Is it possible to add missing atoms in residues using gromacs ? ( PS. i already tried pdb2gmx but it didn't work out) missing atoms are : GLU A 117CB CG CD OE1 OE2 PRO A 158CB CG CD Thank you! -- *Rahma Dahmani Doctorante en CHIMIE