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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/13 5:10 PM, aixintiankong wrote:
Dear,
First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+
and a ligand. when i check the charge of NAD+, I find that the distribution
of charge is not correct, the N1N atom should be positive charge but the
chimera give a negative. so
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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How do GAFF and acpype work?
Mark
On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote:
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
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 Wassenaar)
5. PhD vacancy on MD modelling at University of Groningen
(Patrick Onck
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 .
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,
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
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
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!
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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 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
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
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,
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
Please read trjconv -h.
-Justin
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 aixintiank...@126.com wrote
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 aixintiank...@126.com 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
At 2013-04-14 11:07:39,aixintiankong aixintiank...@126.com 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
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
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
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 !
--
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,
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,
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 aixintiank
: aixintiankong aixintiank...@126.com
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
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From: aixintiankong aixintiank...@126.com
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
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