Re: [gmx-users] Percentage of potential SASA of ligands in Gromacs??

SASA(exposed component) = SASA(system) - SASA(system minus component) + SASA(component) See https://twitter.com/dr_dbw/status/1121554245688250369 for a diagram. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381

[gmx-users] GMX CURRENT

Hi everyone, I am using gmx current in 2018.2 version to get the static conductivity through the Einstein Helfand fitting, however, I am not understanding the output. In the output there are some informations such as the value of the Prefactor fit E-H: 1 / 6.0*V*k_B*T, that following the

[gmx-users] PCA analysis and comparing extreme1 pdbs of two different simulations

Dear all, I am interested in carrying out PCA analysis on two trajectories- 1) protein in water and 2) protein with ligand in water. I would like to know, if there is a procedure by which we can compare the extreme1 pdbs (constituted by the movements that contribute to EV1) from both the

[gmx-users] gmx select

Hi all, I'm trying to work out how many molecules of ligand and water I have within a certain distance. I used the gmx select command below: gmx select -f trajectory.gro -s trajectory.tpr -oi index.dat -select 'resname LIG and within 0.5 of whole_res_com of resnr 1' -dt 100 However, this only

[gmx-users] Generation of force field for "NME " capping group

Dear Gromacs users, I want to capped the end groups of a protein chain with acetyl (ACE) and amine (NME) groups. As I am using gromos96 43A1 force field and NMe is not present in aminoacid.rtp. In amber NME is present but not in gromos. Anyone please suggest something how to generate force

[gmx-users] Best method to calculate binding free energy with GROMACS version 2016.3

Hi everyone, I've run several simulations with a set of 6 ligands and an enzyme (30 ns) in water. I want to employ a method to calculate binding free energy of the ligands but I'm aware that MMPBSA is not compatible with version 2016.3. The forcefield I've used is charmm36-nov2018.ff. I know I

[gmx-users] Box dimension in Umbrella Sampling

Dear users, I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. I understand why for a pull of 5nm, the z axis of the box is set at 12 nm, but did not get

Re: [gmx-users] Failed to realloc error

Hi Mark, I opened a new ticket with the number 2932 and added you in. If you need any other files, please don’t hesitate to contact me. Thank you in advance! With kind regards, Maxim - Maxim Noel Brodmerkel PhD Student, Marklund Group

Re: [gmx-users] clFFT error on iMAC 2017, Gromacs 2019.2, Intel Core i5, GPU Radeon Pro 555 2GB

Hi, That unfortunately looks like Apple's OpenCL not playing well with the clFFT OpenCL library. Avoiding offloading PME to the GPU will allow using GPU acceleration, I think. Can you please try to run a simulation manually and pass "-pme cpu" on the command line? Can you also please file a

Re: [gmx-users] 2019.2 build warnings

Hi Alex, On Wed, Apr 24, 2019 at 9:59 PM Alex wrote: > Hi Szilárd, > > We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is > most certainly there. OK. Can you please post the content of the directories of tests that failed? It would be useful to know the exact software