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 parame
5 jun 2012 kl. 16.52 skrev Thomas Piggot:
> Hi,
>
> I think Erik meant to say that the program is trjorder (not g_order) for the
> ordering of molecules by distance.
>
> Cheers
>
> Tom
Indeed I did. Sorry, and thanks for the correction.
Erik
>
> On 05/06/12 14:41, Erik Marklund wrote:
>>
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 selec
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
redefin
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. Theref
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)?
http:
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
1)
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
cores)
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 "amber99sb.ff/ions.
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 topolog
On 6/6/12 7:36 AM, Amir Abbasi wrote:
*From:* Justin A. Lemkul
*To:* Amir Abbasi ; Discussion list for GROMACS users
*Sent:* Wednesday, June 6, 2012 3:58 PM
*Subject:* Re: [gmx-users] Atomtype OW_tip4p not foun
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 wa
ial type of multithreading called "clustered
>> multithreading". This is slightly similar to the Intel cores with
>> Hyper-Threading.
>>
>>
>> Cheers,
>> --
>> Szil?rd
>>
>>
>>
>> On Mon, Feb 20, 2012 at 5:12 PM, Sara Campos wrote:
>
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 bet
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 cut-o
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 1
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 th
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 ans
Hi,
On Wed, Jun 6, 2012 at 12:13 AM, Justin A. Lemkul 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 z<12.24 nm.
>> I have tried the following:
>>
>> g_sel
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)- phis)) except the
difference that function type 9 is used to handle the multiple potential
functions
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 be
gt; Protein_chain_A 1
>> LIG 1
>> POPC 128
>> SOL 1829
>>
>>
>>
>
> OK, that makes sense. Did InflateGRO remove any lipids? If it did, that is
> not
> reflected correctly in the topology.
No it did,n
In God We Trust
Hello Dear gmx-users
I want to simulate oliver oil by Gromacs. I made topology of triolein with
G45a3 force field at NPT ensemble (according to SCHULER paper ; Journal of
Computational Chemistry, Vol. 22, No. 11, 1205–1218 (2001).I
generated a box with 216 triole
On 7/06/2012 4:33 AM, ramesh cheerla wrote:
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)- phis)) except
the difference that function type 9 i
Hello All,
I have a doubt regarding -tsham option of g_sham (single histogram
analysis). While using g_sham do we need to mention the temperature at
which simulation were performed or it should be the constant (298.15K) for
all analysis ( no matter at what temperature simulations were performed).
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