On 6/09/2012 3:56 PM, Rajiv Gandhi wrote:
I want to calculate the time dependence of the average number
of interfacial water molecules in dimer protein ( example hemoglobin),
In experimental results proposed that the water molecules get
increase/decrease on time scale manner. Is't possible to sh
I want to calculate the time dependence of the average number
of interfacial water molecules in dimer protein ( example hemoglobin),
In experimental results proposed that the water molecules get
increase/decrease on time scale manner. Is't possible to show up this
process in MD simulation studies.
On 6/09/2012 1:02 PM, Marcelo Depolo wrote:
But if you could simulate the environment just around the ligand, then you
could calculate H-bond and angles energies in a quantum perspective. The
limitation is the lack of integration time,
Or am I too wrong?
Sure, any problem you might treat with
I have been avoiding TI or FEP as I doubt my ligand parametrisation is good
enough to warrant the effort. What I am trying to do is get a rough method
working as a secondary screen in a lead optimisation effort. I am not trying
to be perfect, I am just trying to be better than docking at this point
But if you could simulate the environment just around the ligand, then you
could calculate H-bond and angles energies in a quantum perspective. The
limitation is the lack of integration time, but that can be avoided using a
frame that corresponds to the average system pose.
Or am I too wrong?
--
On 6/09/2012 12:15 PM, Marcelo Depolo wrote:
I am not from the area but I believe that a quantum approach is needed for
proper validation of protein-ligand complex.
Use Gromacs in order to lead you to the best frame (or pose), but calculate
the energies in a quantum perspective.
Well that would
On 6/09/2012 12:08 PM, Tom Dupree wrote:
I am trying to differentiate between several binding poses for a protein
ligand complex.
Then you need to measure the free energy differences between them. No
single configuration is ever going to tell the whole story, and maybe
not even a part of it.
I am not from the area but I believe that a quantum approach is needed for
proper validation of protein-ligand complex.
Use Gromacs in order to lead you to the best frame (or pose), but calculate
the energies in a quantum perspective.
It probably wasn't a useful comment but i did anyway =)
Good lu
I am trying to differentiate between several binding poses for a protein
ligand complex.
Initially I tried the LIE method however its results do not followed the
expected trend based on experimental data. I then looked at the raw
interaction energies between the ligand and its environment (LIG-rest
All right, I see. Thank you.
Lingyun
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of XAvier Periole [x.peri...@rug.nl]
Sent: Wednesday, September 05, 2012 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-user
I believe martinize looks for chain identifiers. There is a column for
that in the PDB format.
The other solution is to proceed in two steps ... one chain at the
time ...
On Sep 6, 2012, at 1:22 AM, Lingyun Wang wrote:
Hi XAvier,
Thank you for your reply.
I also tried " python martiniz
GROMOS 54A7 angle types ga_13 and ga_15 seem to be both applicable to
(straight or branched) aliphatic compounds. The force constant is the same
but the equilibrium angle slightly differs from 109.5 to 111.0 degrees. I
suppose that this difference accounts for the steric hindrance that makes
the an
Hi XAvier,
Thank you for your reply.
I also tried " python martinize.py -f complex.pdb -o complex-martini.top -x
complex-martini.pdb -sep", but it still turns out the same result. There is
"Ter" after each chain in the pdb, do I need other way to define that they are
two chains? Thanks.
Best
You may want to try the forum on rte cgmartini.nl for more ...
In short:
try "martinize.py -h" it should give you options to separate the chain
topologies. If it does not work that means your chains are not defined
as two in the input.
Their is not direct manner to CG a lipid file ... the
Hi Chris,
thank you for your answer.
Let me comment on some of your hints.
refcoord_scaling is only required when you are also using positions restraints.
Therefore we need to know what exactly you are doing with position restraints
in order to provide the most useful advice.
Yup, that's right,
Hi all,
There are two chains in the complex.pdb file, but martinize.py only recognize
them as one chain. What can I do to generate two chains in the
complex-martini.top file? My command is as following:
"python martinize.py -f complex.pdb -o complex-martini.top -x
complex-martini.pdb"
By th
As a side note: I would be very interested to know what type of artefacts one
might expect when using refcoord_scaling=no with pressure coupling. I have no
doubt that the description in the manual is accurate, but it is also kind of
cryptic to those of us who don't already understand it.
Thank
Could be a result of not setting x/y compressibility = 0 as the manual
suggests you should do...
On 2012-09-05 11:28:30AM +, 김현식 wrote:
>
> Dear Experts
> Hello.
> I have tried to run md simulation with wall option, which included "nwall=2".
> However, there have been some problems. Always,
refcoord_scaling is only required when you are also using positions restraints.
Therefore we need to know what exactly you are doing with position restraints
in order to provide the most useful advice.
Nevertheless, you ran 2 simulations and got different results. It is not
prudent to
assign the
Dear Experts
Hello.
I have tried to run md simulation with wall option, which included "nwall=2".
However, there have been some problems. Always, the running is down with no
error message or a message like below.
---Program mdrun_mpi_d,
VERSI
Hi everyone,
Just so people know, I have added to the user contributions section of
the website to include the AMBER ParmBSC0 nucleic acid parameters in
GROMACS 4.5.x format (see http://mmb.pcb.ub.es/PARMBSC0/ for further
details regarding these nucleic acid parameters). The modified dihedral
Hi Marcelo,
thanks a lot for your help!!
> After doing the 'pdb2gmx', created the cell e filled with solvent, use the
> "make_ndx" to create an index of your system. One of the groups should be
> your residues that you want to freeze. Then, in your .mdp file, use
> 'freezegrps' and 'freezedim' in
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