Re: [gmx-users] RMSF analysis

? --* I measured Just C-alpha atoms.* Let me know On Wed, Oct 9, 2013 at 9:47 PM, Justin Lemkul wrote: > > > On 10/9/13 3:29 PM, Sainitin Donakonda wrote: > >> Hi all, >> >> I recently performed MD simulation of protein - ligand complex..and >> analyzed its t

[gmx-users] RMSF analysis

Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can a

Re: [gmx-users] Issue in ligand gyration analysis

; On 8/23/13 3:25 AM, Sainitin Donakonda wrote: > >> Hello, >> >> I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to >> analysis this complex using g_gyrate. >> >> Used following command >> >> g_gyrate -s MD_first10.tpr -f Fil

[gmx-users] Issue in ligand gyration analysis

Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate. Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyr

[gmx-users] Problem in Gyrate analysis

Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate. Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyr

Re: [gmx-users] Problem with PME in LIE

I started MD very recently dont have much experience you said i would need .tpr file which doesnot use PME ? how can i get that ? Thanks, Nitin On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul wrote: > > > On 7/17/13 10:43 AM, Sainitin Donakonda wrote: > >> Ok..thanks...so

Re: [gmx-users] Problem with PME in LIE

-rerun option...in help manual it is mentioned that "Neighbor searching will be performed for every frame, unless nstlist is zero".. should i set nslist to zero in MDP file? Thanks On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul wrote: > > > On 7/17/13 10:12 AM, Sainitin Donakonda

Re: [gmx-users] Problem with PME in LIE

Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools .. thanks, nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul wrote: > > > On 7/17/13 9:21 AM, Sainitin Donakonda wrote: > >> Hi justin, >> &g

Re: [gmx-users] Problem with PME in LIE

should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Thanks, Nitin On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul wrote: > > > On 7/17/13 8:54 AM, Sainitin Donakonda wrote: > >> Hi , >> >> I want to use g_lie for

[gmx-users] Problem with PME in LIE

Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is

[gmx-users] Re: Problem with energy minimization parameters

at 5:05 PM, Sainitin Donakonda wrote: > Hi all, > > I have 3 protein-drug complexes (same protein and different drugs) i > performed 20 ns molecular dynamics simulation..using same parameters (i > mean energy minimzation parameters) ..2 of them was successful for MD > simulation

[gmx-users] Problem with energy minimization parameters

Hi all, I have 3 protein-drug complexes (same protein and different drugs) i performed 20 ns molecular dynamics simulation..using same parameters (i mean energy minimzation parameters) ..2 of them was successful for MD simulation..(im using Charmm 27 Force field) But 1 drug protein complex is fa

[gmx-users] Issue with g_lie

Hi Everybody, I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE an

Re: [gmx-users] Issue in Energy minimization protein-ligand complex

, Justin Lemkul wrote: > > > On 7/4/13 3:00 PM, Sainitin Donakonda wrote: > >> Hi all, >> >> I have set of 5 different drugs which are complexed with same protein >> (homology model). So i wanted to run MD simulation using gromacs. I >> followed one pro

[gmx-users] Issue in Energy minimization protein-ligand complex

Hi all, I have set of 5 different drugs which are complexed with same protein (homology model). So i wanted to run MD simulation using gromacs. I followed one procedure as follows 1) I took homology model and minimized it 2) Then followed general procedure of simulation in gromacs. 4 drugs with

Re: [gmx-users] Issue with RMSD for protein drug complex

Hi Justin, Thank your very much for reply i have done both ways i also have backbone RMSD data so i will consider only this in my analysis. Cheers, Sainitin On Thu, Jul 4, 2013 at 3:50 PM, Justin Lemkul wrote: > > > On 7/4/13 5:17 AM, Sainitin Donakonda wrote: > >> Hi all

Re: [gmx-users] Visualize Protein ligand complex

he number of frames. > > Cheers, > > Tsjerk > > > On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger < > kronenberg...@gmail.com> wrote: > > > Don't you wanna try to use the VMD > > > > use vmd xxx.gro yyy.trr and then you could highlight your l

[gmx-users] Issue with RMSD for protein drug complex

Hi all, I ran 20ns simulation on protein drug complex..now i want to check overall stability of this complex to acheive this i did following i supplied index file and choose Protein_Lig option for both least square fit and RMSD calculation..i used following command g_rms -f em.tpr (intital struct

[gmx-users] Visualize Protein ligand complex

Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions with protein binding site I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge with solvent molecules so pymol couldnot visualize com

[gmx-users] Problem in RMSD plot

Hi, Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2 parts first i ran 10ns and extended to another 10ns.. Then I got 2 .xtc files...i combined both these trajectories using following command trjcat -f 1.xtc 2.xtc -o combine.xtc -cat Then using combine.xtc i plotted RM

Re: [gmx-users] Increasing performance of siumulation in cluster

, Mark Abraham wrote: > There are lots of things you might do, but when we don't know what's in the > simulation or anything about the hardware, nobody can tell. > > Mark > > > On Thu, May 30, 2013 at 2:16 PM, Sainitin Donakonda >wrote: > > > Hi all, >

[gmx-users] Increasing performance of siumulation in cluster

Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_firs

[gmx-users] Increasing performance of siumulation in cluster

Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_firs

Re: [gmx-users] Issue running gromacs in Cluster

saving 200 steps? or some thing else Thanks, Sainitin On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard < richard.broadben...@imperial.ac.uk> wrote: > > > On 13/05/2013 08:46, "Sainitin Donakonda" wrote: > > >Hello, > > > >I am trying to run 20

[gmx-users] Issue running gromacs in Cluster

Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500; max

[gmx-users] Problem with DSSP

Hello, I am trying to secondary structure analysis using DSSP in gromacs so i followed this procedure First I downloaded dssp wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O ~/dssp this gave dssp executable file in my home directory I checked ./dssp ...it works Then i s

[gmx-users] Issue with RMSD profile

Hello all, I ran 10ns molecular dynamics simulation of protein ligand complex ..in which protein homology model..finally i analyzed .xtc file which is produced after MD production run..first i plotted RMSD profile of backbone of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from

[gmx-users] Problem with gromacs in Cluster

Hey all, I recently ran 20ns simulation of protein ligand complex on cluster i used following script to run simulation grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_test.tpr mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 *I saved this as MD.sh And then submited