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From: aixintiankong
Date: 2013-02-16 23:54:51
To: gmx-users@gromacs.org
Subject: some waters in active site of receptor
Dear,
there are three waters in active site of receptor, mediating the binding
of ligand with target protein. i want to
: aixintiankong
Date: 2013-02-16 23:54:51
To: gmx-users@gromacs.org
Subject: some waters in active site of receptor
Dear,
there are three waters in active site of receptor, mediating the binding
of ligand with target protein. i want to study the three waters how to affect
the binding of ligand
: aixintiankong
Date: 2013-02-16 23:54:51
To: gmx-users@gromacs.org
Subject: some waters in active site of receptor
Dear,
there are three waters in active site of receptor, mediating the binding
of ligand with target protein. i want to study the three waters how to affect
the binding of ligand
7; to
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Dear,
I have install intel icc and ifor on my system centos, and i want to install
gromacs4.6.1 using the intel icc and ifor,please help me what flag i should use
to indicate the icc and ifor when i install the gromacs.
thank you very much!
At 2013-02-21 13:00:55,aixintiankong wrote
Dear,
when i make MD of my system, i set the MD stop ater 3ns. however, when the
gromacs stop , i find that the system of protein and ligand is not equilibrium,
i want to continue the process to 5ns. but i don't konw how to do this.please
help me.
thank you very much!
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Dear,
In my system ,there are many disulfide bonds in my protein.
i want to split these disulfide bonds to CYSH.
I use these command, pdb2gmx -ignh -f 1AKI.pdb -o 110.pdb -p 110.top -water
spce -ss ,but i get the CYS2.
please help me ,thank you very much!
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Dear,
I have made a 75ns prodution MD, I want to extract frames from the
molecular dynamics simulations at regular intervals of 10ps and keep the file
as individual pdb file. i want get many individual pdb files.
colud anyone can tell me how to perform the command?
thank you !
--
gm
Dear,
In my system ,the loop is part of the active pocket of the protein.
when the ligand is absent, the loop is disordered and if the ligand is present
, the loop can transform into helix. i don't know how to the simulate the state
of the shape of the loop at the different the situatio
At 2013-04-14 11:07:39,aixintiankong wrote:
Dear,
I have made a 10ns prodution MD, I want to extract frames from the
molecular dynamics simulations at regular intervals of 10ps and keep the file
as individual pdb file. The dt=0.002，nstxtcout = 500，i want to use the
follow
Dear,
I have made a 10ns prodution MD, The set dt=0.002，nstxtcout = 500 in
mdp file. I have made 10ns prodution MD, I want to extract frames from the
molecular dynamics simulations at regular intervals of 10ps and keep the file
as individual pdb file i want to use the follow command
Dear,
i have extracted 1000 frames from MD.xtc file. i found the relative
postion of them is very diffrent . so i want to align them and keep them .
please help me
thank you
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Dear,
After extracting the frames of the steep 20th pdb file and 993th pdb file
from the MD, i found the position of the two frames are very diffrent in pymol
and vmd. why? could i exracting pdb file form different steeps and keep them
in align? please help me .
thank you very much!
Dear,
After extracting the frames of the steep 20th pdb file and 993th pdb file
from the MD, i found the position of the two frames are very diffrent in pymol
and vmd. why? could i exracting pdb file form different steeps and keep them
in align? please help me .
thank you very much!
--
?
thank you for you help!
>On 4/21/13 7:40 AM, aixintiankong wrote:
>> Dear,
>> i have extracted 1000 frames from MD.xtc file. i found the relative
>> postion of them is very diffrent . so i want to align them and keep them .
>> please help me
>
>P
Dear Justin,
i really need you help and i will wait for your help ! i am a newer and there
anyone can help me , i hope the frames extracted from a MD can align. i
really don't know why this happen.
thank you very much!
At 2013-04-21 21:47:36,aixintiankong wrote:
Dear,
could you
Dear Justin,
i really need you help and i will wait for your help !
thank you very much!
At 2013-04-21 21:47:36,aixintiankong wrote:
Dear,
could you tell me more detailed about to extract frames from a MD to align.
i try the follow command,but it does not work,
trjconv -s topol.tpr -f
Dear ,
I want to use charmm force field to simulate the protein and ligand
system. The protein can selcet charmm27 in gromacs, but i don't konw how to get
the charmm force field for the ligand. could tell me a simple way to get the to
Topology file for the organic molecule .
thank you !
Dear,
In my system ,the loop is part of the active pocket of the protein. when
the ligand is absent, the loop is disordered and if the ligand is present , the
loop can transform into helix.
In order to simulate the disordered loop transform into helix , i should
build a model thant the l
Dear prof.
i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use
the do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg to analyze the secondary structrue of the protein.
when i perform the do_dssp and select MainChain , the fatal er
Dear,
i want to study how ligands change the conformations using the gromacs
software and i want to run 100ns, but i don't konw how to reasonably set the
nstxout nstvout nstenergy nstlog and nstxtcout.
Thank you very much!
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Dear,
Please help me . i want to simulate a systme of the protein covalently bind
with a organic molecule. Part of the model is standard resides and the rest it
is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i
don't know how to get the topology of the model.
Dear,
Please help me . i want to simulate a systme of the protein covalently bind
with a organic molecule. Part of the model is standard resides and the rest it
is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i
don't know how to get the topology of the model.
i want to study how ligands change the conformations using the gromacs
software and i want to run 100ns, but i don't konw how to reasonably set the
nstxout nstvout nstenergy nstlog and nstxtcout.
Thank you very much!
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
Dear,
In the MD, I find that when the ligand keep in the active site , the
channel formed by two loops is closed. without the ligand the channel is
opened. I don't know how to describe the change of channel. could i describe
the channel by calculating the the most narrow distance(mass ce
Dear,
In the MD, I find that when the ligand keep in the active site , the
channel formed by two loops is closed. without the ligand the channel is
opened. I don't know how to describe the change of channel. could i describe
the channel by calculating the the most narrow distance(mass ce
Dear，
when i keep the ligand in the active site, I use the g_dist calculate
the distance of two residues from two different loops. i look the sticks model
of the two residues by pymol and find that there is a gap between the two
residues. after using g_dist calculate the distance, i
i want to analyze the change of secondary structure of the mainchian frome
residue 20 to residue 60. so i want to make a index file that only contain the
maninchian+H from residue 20 to residue 60. i have inputed the command "
make_ndx -f em.pdb -o index.ndx", but i don't kown how to do next .
s digest..."
>
>
>Today's Topics:
>
> 1. RE: average pressure of a system (Dwey Kauffman)
> 2. how to make a index file (aixintiankong)
> 3. RE: RE: average pressure of a system (Dallas Warren)
> 4. Re: RE: average pressure of a system (Tsjerk Wasse
Dear prof,
can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand
and then use acpype to generate GAFF force field parameter for the NAD+ and
ligand?
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>Message-ID:
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>Content-Type: text/plain; charset=ISO-8859-1
>
>How do GAFF and acpype work?
>
>Mark
>
>On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong wrote:
>> Dear prof,
>> can i use the RESP charge for the cofactor NAD+ a
>
>
>--
>
>Message: 2
>Date: Mon, 23 Sep 2013 21:26:15 -0400
>From: Justin Lemkul
>Subject: Re: [gmx-users] The charge of cofactor and ligand
>To: Discussion list for GROMACS users
>Message-ID
Dear prof.,
i want install gromacs on a multi-core workstation with a GPU(tesla c2075),
should i install the openmpi or mpich2?
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