[gmx-users] simulation in vaccum

Hello Everyone, I am trying to pull ligand biotin out of the streptavidin protein.Following the tutorial Protein ligand complex by Justin ,i have done till energy minimization step skipping adding solvent and ion step,and skipping pressure and temperature equilibration.Now how to proceed further t

[gmx-users] afm simulation

Hello everyone, I am trying to calculate the rupture force between streptavidin and biotin.Firstly,i have calculated the force by placing my complex in water.Now,i want to simulate my complex without placing it in water and then to calculate the rupture force.Can someone tell me,how to simulate a

[gmx-users] Index file

Sorry,I did not realized about archive.Yess,It has solutions for many errors occuring in gromacs. But the problem I am facing now is that i made index.idx file.Like in your tutorial i merged my protein and ligand group. And the output is somewhat like this [ System ] 12345

[gmx-users] (no subject)

Hello, when executing this command g*rompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr d ,fatal error is giving that "Group reference not found in indexfile.* " Why am i getting this error?? Thanks. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] NVT simulation

hello Justin, I am running NVT simulation for 20,000 steps.From last 40 minutes,It is showing on the screen NOTE: Turning on dynamic load balancing and no further steps are shown.Do generally NVT simulation takes a good amount of time or am I making a mistake somwhere in the parameter file? Thanx

[gmx-users] nvt equilibration

Hello Justin, I am curious to know that why have nvt equilibration is not performed in umbrella sampling? Thanx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searc

[gmx-users] Fwd: afm simulation

-- Forwarded message -- From: swati patel Date: Sat, Nov 19, 2011 at 3:18 PM Subject: afm simulation To: Discussion list for GROMACS users Hello Justin, I am following your tutorial on umbrella sampling.My project is on afm simulation of streptavidin-biotin complex.Till

[gmx-users] afm simulation

Hello Justin, I am following your tutorial on umbrella sampling.My project is on afm simulation of streptavidin-biotin complex.Till index.idx i ve created all my files.But as per your tutorial you have discussed of frames extraction and configurations.Since i am dealing with pull afm,so do I also

[gmx-users] fatal error occuring.

Hello Justin, Somehow I obtained ligand and protein topology in charmm force fields. After command grompp,I am getting an error "No such moleculetype LIG" where lig is my ligand abbreviation. Any suggestions for my error?? Thanx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.

[gmx-users] PRODRG server

Hello Justin, Sorry for again and again bothering you.But in prodrg2.5 server,there is no option to choose force fields.It automatically generates topology in gromos 87 force fields. I am using 4.5 version of gromacs in which gromos force fields are gromos 96.How to match my protein and ligand to

[gmx-users] difference in forcefields.

Hello Users, I am facing a problem in obtaining topologies for my ligand.I tried working on acpype,bt it seems very complex to me.PRODRG is easy but it uses gromos87 force field.PRODRG 2.5 is still not available for download. can anyone suggest me how to obtain topologies for my protein and ligan

[gmx-users] problem obtaining similar force fields for protein and ligand

Hello Users, I am facing a problem in obtaining topologies for my ligand.I tried working on acpype,bt it seems very complex to me.PRODRG is easy but it uses gromos87 force field.PRODRG 2.5 is still not available for download. can anyone suggest me how to obtain topologies for my protein and ligan

[gmx-users] PRODRG2.5 server not found.

Helo Justin, The link for prodrg 2.5 server is i.e. http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta is 404 not found.How should I proceed further? Thanx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] difference in force fields.

helo justin, yess since i am dealing with a complex,so i generated protein topology using gromos96 43a1 force fields and for ligands,obtained topology using PRODRG which uses gromos 87 force fields. How to obtain similar force fields topologies since PRODRG only works with gromos87 force fields a

[gmx-users] fatal occur occuring

hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with antic

Re: [gmx-users] GROMACS/ORCA QMMM

hello, I am trying to simulate streptavidin tetramer-biotin complex.I ve calculated Ligand topology from a sofware PRODRG using gromos87 force fields.After solvating it,I am getting an error using grompp command Fatal error: Atomtype HW not found can anyone provide me some help? Thanx with antic