[gmx-users] Problem with OPLS parameters (too few parameters on line)

Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I followed the chris neale directives to make the necessary changes i.e. sigma and epsilon, I incorporated the modified atom types of lipids in o

[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation

Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I wanted to modify the parameter files of lipids taken from peter teilman site. Taking cue from chris neale (may 2006 gmx mailing list) I changed

[gmx-users] Problem with generating topology file for OPLS force field for membrane protein simulation

Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I have previously rum the membrane protein simulations using 43a6 force field with the help of justin's tutorial which had run quite fine. But I a

[gmx-users] installation problem of gromacs 4.0.7 on Rocks cluster

Dear Gmx Users, I am facing problem while installing gromacs 4.0.7 on the rocks cluster 1. command: ./configure --enable-float --enable-threads --enable-sse --enable-mpi we got the following error: checking for cc... cc checking for C compiler default output file name... a.out checking whether t

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 107

Thanks for the reply Justin, > > In theory, that should work. Please post the entirety of your .mdp file. > > Have you done any prior equilibration, or have you moved straight into > annealing? I would suggest a restrained NVT before applying NPT or > annealing > when using the restraints. >

[gmx-users] problem with lipid membrane

fine = -DPOSRES -DPOSRES_LIPID ; restrain protein and lipid P8 -- Maybe there is some problem I am not able to figure. Thanks. Parul Parul tew wrote: > Dear Gmx users, > > > > I am working on a

[gmx-users] problem with lipid membrane

Dear Gmx users, I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After adding ions I energy minimized the system and used trjconv to remove periodicity. In the equilibration phase the lipid molecules were entering the voids in the solv

[gmx-users] problem of lipid molecules entering voids of solvent during equilibration

Dear Gmx users, I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After preparing my system for simulation I have successfully performed the energy minimization, I am facing a problem at the nvt equilibration phase of 100ps, the lipid molec

[gmx-users] Re: problem during Energy minimization

gmx-users@gromacs.org Dear Gmx users, I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After preparing my system for simulation I have successfully performed the energy minimization, I am facing a problem at the nvt equilibration phase of

[gmx-users] problem during Energy minimization

Dear GMX users, I am facing problem while doing energy minimization before the molecular dynamic simulation step of a system consisting of protein, membrane, water and 14 ions. The minim.mdp file is as follows -

[gmx-users] problem during energy minimization before MD

Dear GMX users, I am facing problem while doing energy minimization before the molecular dynamic simulation step of a system consisting of protein, membrane, water and 14 ions. The minim.mdp file is as follows -

[gmx-users] problem in energy minimization of the inflted system

Dear GMX users, I am facing problem while doing energy minimization of the inflated system of a protein with membrane. I inflated the system and updated the removed lipids in the topology file. Now I am stuck during the energy minimization state. Below is the .mdp file for minimization. -

[gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

Hi all, first I would like to thank Justin A. Lemkul for the tutorials provided which are very helpful for new users like me. I am doing a membrane protein simulation and now doing packing of the lipids around the protein. I had run the inflategro.pl script and and now I am facing a problem doing e

[gmx-users] how to define the box when protein protruding out of the lipid bi layer membrane

the protein I am working on is a very large transmembrane protein. I used the DPPC bi layer membrane from peter teilman site and moved my protein into the membrane using VMD. the protein being very big is protruding out of the lipid membrane. Now I want to solvate my whole protein for simulation st

[gmx-users] Atomtype HW not found when using grompp for energy minimization

Hello, I get the following error when I try to run grompp cpmmand for energy minimization in GROMACS of DPPC membrane ... checking input for internal consistency... processing topology... -