dear sir,
I want to do Molecular Dynamics Simulations use gromacs,but I can not find
cardiolipins(CL) parameters. can you Provide cardiolipin pdb file and
parameter(*itp) file?Which is better united atom force field. thank you very
much!
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On 9 May 2014 09:14, gejingming 531015...@qq.com wrote:
I can not find something I want to ! can you help me?
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发件人:
thanks a lot for your reply!
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发件人: 我自己的邮箱;531015...@qq.com;
发送时间: 2014年5月9日(星期五) 下午3:01
收件人: gromacs.org_gmx-usersgromacs.org_gmx-users@maillist.sys.kth.se;
主题: [gmx-users] can you Provide cardiolipin parameter file?
dear sir,
I want to do
Cardiolipin (CL), the signature phospholipid of a
mitochondrion,has broad mitochondrial activities.
The molecular formula:C81H138O17P2.
thanks a lot!
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发件人: Tsjerk Wassenaar;tsje...@gmail.com;
发送时间: 2014年5月9日(星期五) 下午3:37
收件人: Discussion list for
Hi,
Here is a CG one:
http://lipidbook.bioch.ox.ac.uk/package/show/id/31.html
and here is an atomistic one:
http://lipidbook.bioch.ox.ac.uk/package/show/id/61.html
The atomistic one was used in a bacterial membrane, so you will likely have to
change the tails to make an appropriate
Dear Justin
thanks for your quick reply
i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i
choose 1ZE9 as pdb my choice is correct or i have to pdb of protein without
cation for my work or can i delete zinc ion effect in that pdb? for force
field choosing ,i think Opls is
Dear users,
I am running membrane protein simulation in lipid environment. when I
processed through pdb2gmx
*pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc*
*I get the following out put and error. *
*please n*
*help*
Select the Force Field:
From
Hi,
I used ffgmx.itp. It contains CB.
BR,
Samuli Ollila
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of David Ackerman
[da...@cornell.edu]
Sent: Wednesday, May 07, 2014 10:30 PM
thank you very much for your reply!
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发件人: Piggot T.;t.pig...@soton.ac.uk;
发送时间: 2014年5月9日(星期五) 下午5:23
收件人: gmx-us...@gromacs.orggmx-us...@gromacs.org;
主题: Re: [gmx-users] 回复： 回复： can you Provide cardiolipin parameter file?
Hi,
Here is a CG one:
Hi David,
Firstly I would say, is there any reason why you need to use the
Berger/Höltje/GROMOS force field combination? There are several other options
available that I can think of which may be easier/better for you. You could use
the Slipids (with an AMBER force field for the protein),
On 2014-05-09 13:47, Piggot T. wrote:
Hi David,
Firstly I would say, is there any reason why you need to use the
Berger/Höltje/GROMOS force field combination? There are several other options
available that I can think of which may be easier/better for you. You could use
the Slipids (with an
On 5/9/14, 6:25 AM, Balasubramanian Suriyanarayanan wrote:
Dear users,
I am running membrane protein simulation in lipid environment. when I
processed through pdb2gmx
*pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc*
*I get the following out put and error. *
*please n*
On 5/9/14, 1:12 AM, elham tazikeh wrote:
Dear Justin
thanks for your quick reply
i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i
choose 1ZE9 as pdb
my choice is correct or i have to pdb of protein without cation for my
work or can i delete zinc ion effect in that pdb?
On 5/9/14, 6:28 AM, mirko busato wrote:
Dear Users,
In my experiment, one petide of troponin protein and many copies of the same
type of monomer, itaconic acid,(negatively charged) are assembled in a virtual
box.
I would like to understand , if there is a method to calculate the
Dear Justin,
Thank you very much for your quick reply,
In my .mdp file I set up energygrps to protein ITA.
(ITA is the group for the Itaconic acid monomers)
After that I tried to launch g_energy command on .edr file.
Is it right?
which energy terms do you suggest me to use for my problem
I mean that it is a bug because you can't make link after build from the
source, although it is easy to work around with it.
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Hi all,
I have the 8-residue peptide and I want to do Molecular Dynamics
simulations at pH 2 (with explicit solvent).
To do this, I added three Hydrogen atoms to two of the 8-residue peptite
(one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the
NH3 for the start terminus
Nice to know that acidic pH simulations are that easy.
Why do you conclude that you achieved pH 2?
Dr. Vitaly V. Chaban
On Fri, May 9, 2014 at 3:45 PM, Turgay Cakmak turgaycakma...@gmail.com wrote:
Hi all,
I have the 8-residue peptide and I want to do Molecular Dynamics
simulations at pH
Hello,
I appreciate all the responses.
I would like to keep my simulations United Atom. And the paper I am basing
my work and parameter files on used ffgmx with the Holtje cholesterol and
Berger parameters for the lipids. Therefore, most of the interactions are
Berger interactions, except for
On 5/9/14, 9:45 AM, Turgay Cakmak wrote:
Hi all,
I have the 8-residue peptide and I want to do Molecular Dynamics
simulations at pH 2 (with explicit solvent).
To do this, I added three Hydrogen atoms to two of the 8-residue peptite
(one Hydrogen to the Glu, two Hydrojen to the Asp). And
On 5/9/14, 9:38 AM, mirko busato wrote:
Dear Justin,
Thank you very much for your quick reply,
In my .mdp file I set up energygrps to protein ITA.
(ITA is the group for the Itaconic acid monomers)
After that I tried to launch g_energy command on .edr file.
Is it right?
which energy terms
On 5/9/14, 8:41 AM, Ooker wrote:
I mean that it is a bug because you can't make link after build from the
source, although it is easy to work around with it.
It's not a bug, it looks like the build target for making links has simply been
removed, likely a consequence of the complete
On Fri, May 9, 2014 at 6:11 PM, Ooker ganuongp...@gmail.com wrote:
I mean that it is a bug because you can't make link after build from the
source, although it is easy to work around with it.
If you are not the super user, you cannot make links.
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Hi All,
In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are
very approximate.
Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm
= vdwradius=0.185 nm
Is it prudent to replace the values in the local vdwradii.dat with the
vdwradii derived from
On 5/9/14, 12:23 PM, rajat desikan wrote:
Hi All,
In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are
very approximate.
Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm
= vdwradius=0.185 nm
Is it prudent to replace the values in the local
Hi there this is my first time posting here so my apologies if I disregard
any general formatting rules! In any event on to my question/problem.
I am fairly new to MD simulations with much more background on the
biological side than the simulation side. That being said, I have been
receiving
On 5/9/14, 1:46 PM, Douglas Grahame wrote:
Hi there this is my first time posting here so my apologies if I disregard
any general formatting rules! In any event on to my question/problem.
I am fairly new to MD simulations with much more background on the
biological side than the simulation
On 5/9/14, 3:35 PM, rajat desikan wrote:
Thanks Justin. I am curious about the value for a phosphorus atom (protein
in phospholipid bilayer; g_sas issues a warning). Do you know any reference
for experimental values?
Google knows.
-Justin
On Friday, May 9, 2014, Justin Lemkul
Do mind that the radius for P in PO4 is different from that for P alone.
Cheers,
Tsjerk
On May 9, 2014 10:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/9/14, 3:35 PM, rajat desikan wrote:
Thanks Justin. I am curious about the value for a phosphorus atom (protein
in phospholipid
Hi All
I am using topo writegmxtop output.top in VMD and it writes fake sort of
top file which needs further user based adjustments.
The top file so generated has all [bonds] [angles] [dihedral] information
but [pairs] are missing. I am using charmm36 which says gen-pair =yes in
forcefield.itp.
On 5/9/14, 7:35 PM, gromacs query wrote:
Hi All
I am using topo writegmxtop output.top in VMD and it writes fake sort of
top file which needs further user based adjustments.
The top file so generated has all [bonds] [angles] [dihedral] information
but [pairs] are missing. I am using
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