[gmx-users] Issue in ligand gyration analysis

2013-08-23 Thread Sainitin Donakonda
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 ***

[gmx-users] Invalid order for directive atomtypes

2013-08-23 Thread afsaneh maleki
Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct graphite.itp file. Generated topology file is as the following: #include ./oplsaa.ff/forcefield.itp #include TP.itp

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

2013-08-23 Thread Justin Lemkul
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 File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives

Re: [gmx-users] Invalid order for directive atomtypes

2013-08-23 Thread Justin Lemkul
On 8/23/13 3:29 AM, afsaneh maleki wrote: Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct graphite.itp file. Generated topology file is as the following: #include

[gmx-users] DMPC Bilayer

2013-08-23 Thread Rama
Hi Justin, Thanks for Kalp15-DPPC Bilayer tutorial. I'm doing MD simulations for MMP protein-DMPC bilayer (128 lipids) complex by following your protocol. I'm not familiar with MD simulation parameters. Should I need to change any parameters in npt.mdp , nvt.mdp and md.mdp files or somewhere

Re: [gmx-users] DMPC Bilayer

2013-08-23 Thread Justin Lemkul
On 8/23/13 9:21 AM, Rama wrote: Hi Justin, Thanks for Kalp15-DPPC Bilayer tutorial. I'm doing MD simulations for MMP protein-DMPC bilayer (128 lipids) complex by following your protocol. I'm not familiar with MD simulation parameters. Should I need to change any parameters in npt.mdp ,

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

2013-08-23 Thread Sainitin Donakonda
Thank justin for reply i also thought same i used gromacs 4.5.5 here so just now i used gromacs 4.5.4 it works perfectly but choosing ligand only gives value as zero..can you tell me what might be the reason ? Thanks, Nitin On Fri, Aug 23, 2013 at 3:12 PM, Justin Lemkul jalem...@vt.edu wrote:

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

2013-08-23 Thread Justin Lemkul
On 8/23/13 9:38 AM, Sainitin Donakonda wrote: Thank justin for reply i also thought same i used gromacs 4.5.5 here so just now i used gromacs 4.5.4 it works perfectly but choosing ligand only gives value as zero..can you tell me what might be the reason ? No idea. What is the ligand?

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

2013-08-23 Thread Chandan Choudhury
Nitin, You can use g_polystat and see if you can reproduce your observations. Chandan -- 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/Search before posting! *

Re: [gmx-users] position restraint

2013-08-23 Thread Mark Abraham
It doesn't work is not enough information to lead anyone to a solution :-) Mark On Thu, Aug 22, 2013 at 6:53 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: If you mean that I need to modify the posre_ion.itp file to: ; position restraints for a_85563 of system [ position_restraints