I am trying to calculate the PMF of a drug inside a membrane protein
which forms a channel. The reaction coordinate is the z-axis. In
order to do so, I would like to use Umbrella sampling of the drug in
many positions along the z-axis, followed by WHAM. That should give me
the PMF for each posi
ASHWINI JAYAPRAKASH wrote:
Hi,
I am a new gromacs user and have problems creating a topology file using
the pdb2gmx command for simulating a six helix bundled alamethecin in
lipid bilayer.
when I use the command :
pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top
I get the error :
Hi,
I am a new gromacs user and have problems creating a topology file using the
pdb2gmx command for simulating a six helix bundled alamethecin in lipid bilayer.
when I use the command :
pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top
I get the error :
Program pdb2gmx, VERSION 3.3.
Hi,
On Jun 19, 2007, at 5:26 PM, Liwei Li wrote:
I want to carry out normal mode analysis on a large protein (about
10,000 atoms) without using coarse grain approximations. Amber is
out of the question since it can only handle about 5,000 atoms for
NMA. I am wondering if GROMACS can deal w
Hi,
I want to carry out normal mode analysis on a large protein (about 10,000
atoms) without using coarse grain approximations. Amber is out of the
question since it can only handle about 5,000 atoms for NMA. I am wondering
if GROMACS can deal with this assuming running on a 64-bit machine with 8
Thanks Pedro,
if I did not misunderstand you I should go for something like this:
pcoupl = berendsen
pcoupltype = surface-tension
ref_p = 600 1.025
tau_p = 5.0 5.0
compressibility = 9.8e-5 4.53e-5
Is it correct?
Hmmm... "Surface tension" is a tricky subject at the microscopic level.
Besides
Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote:
>
>
> "The first ref_p value is the reference surface tension times the
> number
> of surfaces [bar nm],"
>
> I have a lipid bilayer membrane su I guess I should multiply by 2 the
> surface tension value for which I do not h
Hi,
I want to get the radial distribution of my system which is composed of a box
of capped alanine residues (CAR). In this respect, I used g_rdf command with
-com option. I chose one of the CAR s as the first, and the others as the
second group. In manual, for -com option, it is written that t
Dear GMX users,
I am trying to calculate the PMF of a drug inside a membrane protein
which forms a channel. The reaction coordinate is the z-axis.
In order to do so, I would like to use Umbrella sampling of the drug in
many positions along the z-axis, followed by WHAM. That should give me
the PMF
Dear all
I want to insert protein in bilayer. in make-hole
program, what is -r -cx and -cy ? how can i select
them?(they are grasp result or no)
best regards
Building a website is a piece of cake. Yahoo
Hi
I never had to change masses in the nb.itp and I ran lots of simulations
with the amber-Port...Are you sure, that you had no dummies with mass
zero or so?
REgards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am F
Hi.
I want to make a NMA just for one Group of molecules, because a QMMM-NMA takes
too long for the whole system. Of cause, the EM in the step before has been
done for the whole system. The manual does not tell how to do this. Did
someone tried this before?
Thanks
Christian.
--
B.Sc. Christ
Yang Ye wrote:
On 6/19/2007 5:29 PM, Roberto Marchese wrote:
Dear GROMACS Users,
the OPLSAA force field (implemented in gromacs), have a notation for
deprotonated arginine ARGN vs ARG (charge 0). The utility pdb2gmx
don't give do possibility to set arginine protonation state, like LYS,
HIS ..
On 6/19/2007 5:29 PM, Roberto Marchese wrote:
Dear GROMACS Users,
the OPLSAA force field (implemented in gromacs), have a notation for
deprotonated arginine ARGN vs ARG (charge 0).
The utility pdb2gmx don't give do possibility to set arginine
protonation state, like LYS, HIS ...
There are a w
Dear GROMACS Users,
the OPLSAA force field (implemented in gromacs), have a notation for
deprotonated arginine ARGN vs ARG (charge 0).
The utility pdb2gmx don't give do possibility to set arginine
protonation state, like LYS, HIS ...
There are a way to overcome this problem?
I have found at
Hi,
Actually I think that although the .atp file seems to be used, the
masses in the ffamberxxnb.itp file must be changed from the zero values
to the correct ones: when I ran a simulation without changing them I got
infinite velocities and which did nor happen when I changed the masses
to
Hi again!
The end of my top file looks :
[ molecules ]
; Compound#mols
Protein 1
SOL 10682
/Anna
On 6/19/07, Erik Marklund <[EMAIL PROTECTED]> wrote:
19 jun 2007 kl. 09.31 skrev Anna Reymer:
> Dear GROMACS users!
>
> Is it possible to model DNA with the help
Maik Goette wrote:
David
I think, I should not contradict to one of the developers, but if your
statement is true:
1. Where, in fact, are the masses coming from (the masses in the amberFF
port can only be found in the atp, as far as I know)?
2. Why does GROMACS complain about missing atoms in
한상화 wrote:
> Thank you for the comment.
> Any comment on the missing [ angles ] in ffamber03.rtp which is included in
> ffG43a1.rtp?
> May I leave it out when I define a new residue in ffamber03.rtp?
grompp will warn you when there are parameters missing. you will have to
make sure it uses the rig
19 jun 2007 kl. 09.31 skrev Anna Reymer:
Dear GROMACS users!
Is it possible to model DNA with the help of GROMACS with AMBER ports?
I've checked mailing-list and found that the only GROMCAS force field
appropriate for modeling DNA is OPLS, but it does not provide good
enough results for long D
Thank you for the comment.
Any comment on the missing [ angles ] in ffamber03.rtp which is included in
ffG43a1.rtp?
May I leave it out when I define a new residue in ffamber03.rtp?
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of David van der Spoel
Sent:
> Dear GROMACS users!
>
> Is it possible to model DNA with the help of GROMACS with AMBER ports?
> I've checked mailing-list and found that the only GROMCAS force field
> appropriate for modeling DNA is OPLS, but it does not provide good
> enough results for long DNA MD runs.
> The mailing-list sug
> [Question 1] The topology file produced by pdb2gmx with Amber FF
> (ffamber03, for example) looked different from what we used to obtain with
> ffG43a1.
>
> No force constants were assigned in [ bonds ], [ angles ], [ dihedrals ],
> etc.
That's because they're being read from ffamber03bon.itp b
Dear GROMACS users!
Is it possible to model DNA with the help of GROMACS with AMBER ports?
I've checked mailing-list and found that the only GROMCAS force field
appropriate for modeling DNA is OPLS, but it does not provide good
enough results for long DNA MD runs.
The mailing-list suggested AMBER
Mark Abraham wrote:
Yes, that was my mistake - PE energy of the whole system is about 65
thousands kcal/mol. But Protein-Ligand Coul SR energy is in the range of
50-100 kcal/mol, so it seems to me to be strange that it's much higher
than Autodock's predicted value of binding energy.
Is Autodock
한상화 wrote:
> Dear Gromacs users,
>
>
>
> I have successfully installed Amber FF in Gromacs according to the
> instruction by the Pande Group (http://folding.stanford.edu/ffamber/).
>
> I ran a demo successfully and enjoyed the speed of Gromacs.
>
> My questions are:
>
> [Question 1] The top
Dear Gromacs users,
I have successfully installed Amber FF in Gromacs according to the
instruction by the Pande Group (http://folding.stanford.edu/ffamber/).
I ran a demo successfully and enjoyed the speed of Gromacs.
My questions are:
[Question 1] The topology file produced by pdb2gmx with
> Yes, that was my mistake - PE energy of the whole system is about 65
> thousands kcal/mol. But Protein-Ligand Coul SR energy is in the range of
> 50-100 kcal/mol, so it seems to me to be strange that it's much higher
> than Autodock's predicted value of binding energy.
Is Autodock predicting a b
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