There is no GROMACS tool that repairs incomplete structures, but you can
find other programs that can do it. Some of them have been previously
posted in this list (try a search on it). Personally I've used Swiss PDB
viewer, which is useful to add missing atoms.
Javier
El 06/06/12 07:42,
Hello all
I have to do MD simulation of membrane protein having docked ligand in POPC
lipid bilayer.
I am geeting error during solvation of system:
Resname of 1POPC in system_shrink1.gro converted into 1LIG
I have done following:
GROMACS COMMAND
1) Generate topol.top using GROMOS96 53A6
Pymol has similar functionality, in case you prefer that over VMD.
5 jun 2012 kl. 22.23 skrev Peter C. Lai:
You can also use something like VMD where you load the trajectory then
select your atoms, then increment the frames and extract the xyz coordinates
of each of your atoms in the
I use MacroMolecular Builder for all sorts of things, including filling in
missing atoms.
Erik
6 jun 2012 kl. 08.59 skrev Javier Cerezo:
There is no GROMACS tool that repairs incomplete structures, but you can find
other programs that can do it. Some of them have been previously posted in
Dear all gromacs users,
After added the counter ions to the top
file and further i used 'grompp' commond,i got the following error.
Fatal error:
moleculetype CU1 is
It seems that redefinition comes from including tow different ions.itp
files, here:
; Include topology for ions
#include gromos43a1.ff/ions.itp
#include ions.itp
Javier
El 06/06/12 10:51, Seera Suryanarayana escribió:
Dear all gromacs users,
After added
Hi,
I have to questions regarding genion.
1) Is there a possibility to tell genion in advance which group of
molecules to replace by ions (for me, solvent is always the choice so I
want to skript it but I did not find any parameters for this)?
2) I want to neutralize a charged system.
On 6/6/12 5:38 AM, Matthias Ernst wrote:
Hi,
I have to questions regarding genion.
1) Is there a possibility to tell genion in advance which group of molecules to
replace by ions (for me, solvent is always the choice so I want to skript it but
I did not find any parameters for this)?
On 6/6/12 3:09 AM, Sangita Kachhap wrote:
Hello all
I have to do MD simulation of membrane protein having docked ligand in POPC
lipid bilayer.
I am geeting error during solvation of system:
Resname of 1POPC in system_shrink1.gro converted into 1LIG
I have done following:
GROMACS COMMAND
Apologies for reviving such an old thread. For clarifications, interlagos
and bulldozer both have a modular architecture, as mentioned earlier. Each
bulldozer module has 2 integer cores and one floating point unit shared
between the two cores. So, although you have 64 cores (counting integer
Hi!
I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then
I generate .gro and .top files of that with amb2gmx.pl.
I'm manually add this lines to .top file
; Include water topology
#include amber99sb.ff/tip4p.itp
; Include topology for ions
#include
On 6/6/12 7:19 AM, Amir Abbasi wrote:
Hi!
I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I
generate .gro and .top files of that with amb2gmx.pl.
I'm manually add this lines to .top file
; Include water topology
#include amber99sb.ff/tip4p.itp
; Include topology
On 6/6/12 7:36 AM, Amir Abbasi wrote:
*From:* Justin A. Lemkul jalem...@vt.edu
*To:* Amir Abbasi amir.abbas...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
*Sent:* Wednesday, June 6, 2012
Dear Gromacs Users,
Greetings of the day!!
I am simulating a system of Protein-Mg-GTP complex. There are 2 states for
the same, state 1 and state2. The difference lies in the presence of 2
specific H-bonds in the state 2 ,which are absent in state 1.
Now, I need to find the energy barrier that
/Support/Mailing_Lists
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Message: 4
Date: Wed, 6 Jun 2012 04:19:05 -0700 (PDT)
From: Amir
On 6/6/12 8:52 AM, Sangita Kachhap wrote:
On 6/6/12 3:09 AM, Sangita Kachhap wrote:
Hello all
I have to do MD simulation of membrane protein having docked ligand in POPC
lipid bilayer.
I am geeting error during solvation of system:
Resname of 1POPC in system_shrink1.gro converted into 1LIG
Dear Gmx Users,
I created a plane surface made of 4 different atoms (400 atoms togehter).
Each atom correspond to different residue - I added them to the
aminoacids.rtp file. They are placed in different positions with LJ radius
of 1.7A and they their center is 3.6 A away from each other (0.2A
Dear gmx-users,
I have a problem concerning energy conservation when using user potentials
(tables).
I'm using gromacs 4.5.4
I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 chains a 10
beads in a 26x26x26 periodic box).
I tried different vdwtypes (cutoff always 3.24):
The
HI, all,
I want to use MTTK for the pressure coupling for NPT simulation, while
I can not get the correct pressure value.
The following result is a simulation with 1000 SPC-E water molecules
with temperature 303.15K and pressure 1 bar.
Statistics over 101 steps [ 0. through 1000. ps
On 6/6/12 11:07 AM, Bao Kai wrote:
HI, all,
I want to use MTTK for the pressure coupling for NPT simulation, while
I can not get the correct pressure value.
The following result is a simulation with 1000 SPC-E water molecules
with temperature 303.15K and pressure 1 bar.
Statistics over
Hi All,
To be able to get information about the hydrophobic contacts, I prepared
index.ndx which includes 2 groups of atoms that belong to hydrophobic
residues of my system. Then, I used the command
“g_dist -f traj.xtc -s topol.tpr -n index.ndx -dist 0.4 -lt -o
lifetime.xvg” .
which gave
Hi Gromacs Users
I want to plot SAS of residues with errobar.
I want to know what is the meaning of third column in file of residue.xvg
(output of g_sas)?
which of the following expression is true about third column?
1) first answer=sqrt(summation(s_i - s_mean)/(N-1)))
2) second answer= first
Hi,
On Wed, Jun 6, 2012 at 12:13 AM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/5/12 2:55 PM, Andrew DeYoung wrote:
I would like to use g_select_d to generate an index file containing the
atoms of BF4 residues whose centers of mass are in the range z12.24 nm.
I have tried the following:
Dear Mark,
Thank you for your reply, According to my
understanding functional form of dihedral function type 9 is same as
dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the
difference that function type 9 is used to handle the multiple potential
Hi All,
I'm wondering if anyone has experienced what I'm seeing with Gromacs 4.5.5 on
GPU. It seems that certain systems fail inexplicably. The system I am working
with is a heterodimeric protein complex bound to DNA. After about 1 ns of
simulation time using mdrun-gpu, all the energies
dumped)
The Gromacs is installed on the cluster - version 4.5.5. I tried also on
4.5.4. and the same happens.
Could you please advise?
Steven
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