[gmx-users] g_mmpbsa for rna-rna complex

Hi gromacs users, I want to do md simulation of rna-rna complex. Can I do g_mmpbsa tools for calculation of Delta G binding? Best, Atila -- 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

[gmx-users] g_mmpbsa parameter verify: using last 5ns of MD trajectory for binding energy calculation.

Dear Expert, Kindly apologise for putting up a question not exactly related to gromacs. I have a 30ns protein ligand simulation trajectory from Gromacs. I would like to use the last 5ns (i.e 25-30 ns) of the trajectory for binding energy calculation. As mentioned in the g_mmpbasa article i want

[gmx-users] g_mmpbsa

Hii all I want to calculate the binding energy between a biomolecule and ligand. I have tried installing  g_mmpbsa but  my gromacs version is 2016.3. Can I use g_mmpbsa with gromacs-2016.3 or any other way to calculate the binding energy?  Thanks Sunipa -- Gromacs Users mailing list * Please

Re: [gmx-users] g_mmpbsa compilation error

Hi, This does not look like an issue with building GROMACS - g_mmpbsa is not an official GROMACS tool, so you should perhaps inquire elsewhere also. Mark On Fri, Sep 1, 2017 at 11:55 AM neha chaudhary wrote: > Hi, > > I am trying to compile g_mmpbsa with APBS for

Re: [gmx-users] g_mmpbsa compilation error

Likely you cmake is far newer than Gromacs (cmake --version to figure that out). You should try Gromacs 2016.3 On Friday, September 1, 2017, 12:55:14 PM GMT+3, neha chaudhary wrote: Hi, I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS

[gmx-users] g_mmpbsa compilation error

Hi, I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and gromacs installed properly but during cmake for g_mmpbsa I am facing the following error: -- Found z library: /usr/lib/x86_64-linux-gnu/libz.so CMake Error at cmake/FindGROMACS.cmake:203 (list): list index: 2 out of

Re: [gmx-users] G_MMPBSA

Did you try the pre-compiled version from here: http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html it worked just fine with me on debian and CentOS. Offcourse you need to have APBS installed. On Thu, Jul 27, 2017 at 7:04 PM, Mark Abraham wrote: >

Re: [gmx-users] G_MMPBSA

Hi, You should start by reading and following the installation guide of this non-GROMACS tool. If you have questions, asking on its forum is probably best ;-) And please do provide some detail and what you did and where it went wrong. Mark On Thu, 27 Jul 2017 18:14 S M Bargeen Turzo

[gmx-users] G_MMPBSA

Hi all, I am trying to install g_mmpbsa gromacs package( http://rashmikumari.github.io/g_mmpbsa/) but it's not working. Can anyone please guide me through the installation process of this package? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] g_mmpbsa

Hi gromacs users, How to install mmpbsa using cgywin? I am using gromacs through cgywin. Thanks, Kulkarni.R -- 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

Re: [gmx-users] g_mmpbsa python script error

On 7/2/16 9:22 AM, Amali Guruge wrote: Dear All, I installed g_mmpbsa tool for binding energy calculation for my GROMACS runs. When I gave the command, python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg I got the following error. python: can't open file 'MmPbSaStat.py': [Errno

[gmx-users] g_mmpbsa python script error

Dear All, I installed g_mmpbsa tool for binding energy calculation for my GROMACS runs. When I gave the command, python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg I got the following error. python: can't open file 'MmPbSaStat.py': [Errno 2] No such file or directory Please can

[gmx-users] g_mmpbsa

Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule. From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I understand that solvation energy is the sum of polar and nonpolar energies so

Re: [gmx-users] g_mmpbsa positive binding energy

Hi, MM/PBSA method has several limitations (discussed in several publications) and therefore, you may be getting positive energy values from these limitations. You may get a negative binding energy after further increasing the dielectric constant, however, interpretation of this value would be

[gmx-users] g_mmpbsa positive binding energy

Dear Gromacs Users I am trying to calculate binding energy of protein-ligand and protein-receptor complex using g_mmpbsa. I have run simulation of 10 ns and snapshot was generated at every 1 ps. Initial 2ns was not taken. g_mmpbsa was run for the rest of the frames. The command line was given as:

Re: [gmx-users] g_mmpbsa time

You may use -dt as option in g_mmpbsa. For example, -dt 600 or -dt 120 . On Thursday, September 17, 2015 at 7:41:25 AM UTC+2, elham wrote: > > Dear users > i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps > for binding free energy computations by g_mmpbsa method in gromacs,

Re: [gmx-users] g_mmpbsa

Dear Leila IF you want help, you must say it best Cris 2015-09-21 7:00 GMT-03:00 leila karami : > Dear gromacs users, > > Can I use g_mmpbsa tool for calculation of binding free energy in > RNA-ligand complex? > > Best, > Leila Karami > -- > Gromacs Users mailing list >

[gmx-users] g_mmpbsa

Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- 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

[gmx-users] g_mmpbsa

Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- 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

[gmx-users] g_mmpbsa time

Dear users i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps for binding free energy computations by g_mmpbsa method in gromacs, my computations took a long time is it correct? can i change my simulation time in *mdp* file for *tpr* production for using in g_mmpbsa

Re: [gmx-users] g_mmpbsa

On 8/16/15 12:38 PM, elham tazikeh wrote: Dear GMX Users is there anyone to help me in g_mmpbsa using for binding free energy calculation i have questions about *.mdp files as polar.mdp or for instance: what is the value of pdie in protein-ligand combinations i really appriciate for any

[gmx-users] g_mmpbsa

Dear GMX Users is there anyone to help me in g_mmpbsa using for binding free energy calculation i have questions about *.mdp files as polar.mdp or for instance: what is the value of pdie in protein-ligand combinations i really appriciate for any help -- Gromacs Users mailing list * Please

Re: [gmx-users] g_mmpbsa

Hi again, Have you exported the environment variables which tell g_mmpbsa where the necessary GROMACS and APBS files are? This is not necessary for me because I linked everything while compiling, but it must be necessary when using the pre-compiled binaries export APBS=path-to-executable

[gmx-users] g_mmpbsa

Hi, I am new to g_mmpbsa and need some help. I have downloaded very latest 64bit binaries. My machine is 64bit and has ubuntu 14.04. There is problem in binary, I am getting 'core dumped' error all the time. It says: Illegal instruction (core dumped). For example, if I run a test

Re: [gmx-users] g_mmpbsa

Hi, I'm currently using g_mmpbsa without issues. I installed it from the source-code following the instructions in their website. Your error output is Setting option -pdie more than once!Illegal instruction. Try using it without the option -pdie, since it is likely already inside the

[gmx-users] g_mmpbsa

Dear Leandro i really appriciate for your help i used of *Pre-compiled binary* http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html#binary for my work and also i did them without -*pdie*, but i saw that error again. should i change the number of -*pdie* or not? i saw in Input

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Thanks Rashmi. Finally, I have been able to install g_mmpbsa. Apart from the gmx lib files there were issues in installing APBS as well, took a quite amount of time to find the source code of that version that has the lib files needed for g_mmpbsa. Thanks anyways, Sucharita On Mon, Jun 16,

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Hi Rashmi, I am facing difficulty in installing the tool you mentioned g_mmpbsa. I am giving this command: ./configure --enable-gmx46 --with-gmx-include=/usr/local/gromacs/include --with-gmx-lib=/usr/local/gromacs/lib configure: error: Could not find /libgmx.a library file I

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Dear Prof. David van der Spoel, Thank you very much for considering g_mmpbsa for the GROMACS repository. We have a discussion on the same and will try to patch g_mmpbsa in the repository. Presently, we do not know how to integrate compilation procedure of g_mmpbsa with the GROMACS package as APBS

[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Dear GROMACS users, We have developed a new tool, *​​g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses APBS libraries for the Poisson-Boltzmann calculations. ​ ​Features: - ​​ Include SASA, SAV and WCA ​-like​ non-polar models - It inherits threading (OpenMP)

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

On 2014-06-09 21:17, Rashmi wrote: Dear GROMACS users, We have developed a new tool, *​​g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses APBS libraries for the Poisson-Boltzmann calculations. ​ ​Features: - ​​ Include SASA, SAV and WCA ​-like​ non-polar