Re: [gmx-users] Coordinate file does not match topology

Quoting Sheyore Omovie <[EMAIL PROTECTED]>: > But this is my first real simulation, So I'll appreciate it if you can tell > me how to determine the number of ions to add with genion. Assuming you started from a .pdb file of your protein, pdb2gmx prints this information out when you generated your

Re: [gmx-users] Coordinate file does not match topology

Thanks, But this is my first real simulation, So I'll appreciate it if you can tell me how to determine the number of ions to add with genion. Thanks John From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-

[gmx-users] genion

Hi!! I want know because we must neutralize the total load of the system (protein + water) in the interior of the box with genion. Elias ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

Re: [gmx-users] Stuck --> unstuck ...

Stéphane Téletchéa wrote: I've found out where the problem lie (at least one of ...). Small reminder: i've tried to setup a system consisting of HIV protease + one ligand on a water box. I used the excellent protocol from John E. Kerrigan (Drug-enzyme tutorial) in order to set up my simulation

Re: [gmx-users] Regarding mdrun segmentation fault in cluster

[EMAIL PROTECTED] wrote: Selon naga raju <[EMAIL PROTECTED]>: Dear gmx users, I am using mdrun command in pentium-4 redhat linux, job was completed without any errors. When I use the same files in cluster(redhat enterprizes OS), I got the following error, ... gen_seed

Re: [gmx-users] Regarding mdrun segmentation fault in cluster

Selon naga raju <[EMAIL PROTECTED]>: > Dear gmx users, > I am using mdrun command in pentium-4 > redhat linux, job was completed without any errors. > When I use the same files in cluster(redhat > enterprizes OS), I got the following error, ... > gen_seed =17532 > cons

Re: [gmx-users] Regarding mdrun segmentation fault in cluster

naga raju wrote: Dear gmx users, I am using mdrun command in pentium-4 redhat linux, job was completed without any errors. When I use the same files in cluster(redhat enterprizes OS), I got the following error, Grid: 14 x 14 x 15 cells Configuring nonbonded kernels... Testing x

Re: [gmx-users] protein in hole

mahbubeh zarrabi wrote: dear david how can i do by editconf?whould you please help in detail? no. try editconf -h -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular

[gmx-users] Regarding mdrun segmentation fault in cluster

Dear gmx users, I am using mdrun command in pentium-4 redhat linux, job was completed without any errors. When I use the same files in cluster(redhat enterprizes OS), I got the following error, Grid: 14 x 14 x 15 cells Configuring nonbonded kernels... Testing x86_64 SSE2 support..

Re: [gmx-users] protein in hole

dear david how can i do by editconf?whould you please help in detail? --- David van der Spoel <[EMAIL PROTECTED]> wrote: > mahbubeh zarrabi wrote: > > dear freinds > > I have made a hole in POPC128a bilayer and did > mdrun > > for popc(make-hole).i merged protein and popc by > cat > > command but

Re: [gmx-users] protein in hole

mahbubeh zarrabi wrote: dear freinds I have made a hole in POPC128a bilayer and did mdrun for popc(make-hole).i merged protein and popc by cat command but protein did not put in hole in popc.whould you please help me? thanks start with man cat you could try by centering the hole and the protei

[gmx-users] protein in hole

dear freinds I have made a hole in POPC128a bilayer and did mdrun for popc(make-hole).i merged protein and popc by cat command but protein did not put in hole in popc.whould you please help me? thanks Be