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 ***
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
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
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
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
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 ,
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:
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?
Nitin,
You can use g_polystat and see if you can reproduce your observations.
Chandan
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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
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