Dear Neeru Sharma,
I know off hand from years of work with Mg-GTP sites, they are realativly
rigid/staritforward. If the bonds arn't present with occupied GTP, or Mg at
the beggining, you should equilabrate your starting structures more. Unless
your looking at the GTP binding to Mg in which
Dear Gmx Users,
How to recalculate the force constant from the harmonic potential: 1
[pN/A] into [kJ/mol nm2] ? Where is the [mol] here?
Thanks,
Steven
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Hi everybody,
I want to put my protein in a box with the command:
editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2logErr
1logOut
and add solvent afterwards with:
genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
2logErr 1logOut
But when I look at it I see
Hi Shima,
The lipids.rtp file in the charmm36.ff folder has many different entries
for lipids. All you need to do is to run pdb2gmx with just one of your
lipids of interest. This will produce a .top for this one lipid which is
trivial to convert into an .itp (see Chapter 5 of the manual).
Dear Thomas,
It's a good idea. Thanks :)
Sincerely,
Shima
- Original Message -
From: Thomas Piggot t.pig...@soton.ac.uk
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, June 29, 2012 1:39 PM
Subject: Re: [gmx-users] Berger lipid
Hi Shima,
The lipids.rtp
Hi everybody,
I wanted to add water in the box where I put the protein with the command
genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
2logErr 1logOut
The result is that I have indeed water (SOL) in the protein file
(3m71_water.gro). But there is a problem in the topology
Hello
I use a CHARMM27 force field and my system is lumiflavin in water. I use the
spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure
minimization. I made a file pr.mdp. Could you please tell me, what I could do
better in this file, or what is wrong? I guess there
Make sure your top file #include ff/spc.itp
On 2012-06-29 11:35:24AM +0200, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Hi everybody,
I wanted to add water in the box where I put the protein with the command
genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
On 6/29/12 4:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to put my protein in a box with the command:
editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2logErr
1logOut
and add solvent afterwards with:
genbox -cp 3m71_box.gro -cs spc216.gro
On 6/29/12 6:01 AM, Lara Bunte wrote:
Hello
I use a CHARMM27 force field and my system is lumiflavin in water. I use the
spc216 water model, a dodecahedral box with 1.3 nm. I want to make a
CHARMM27 should be combined with TIP3P, not SPC.
structure minimization. I made a file pr.mdp.
yes
http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract
The files are here:
http://uab.hyperfine.info/~pcl/files/popc36/
On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote:
Yes, I remember now...you are right :) But I didn't
Dear Peter,
Thanks a lot :)
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Friday, June 29, 2012 2:54 PM
Subject: Re: [gmx-users] Berger lipid
hi
as suggested in: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
i do:
prompt git clone git://git.gromacs.org/gromacs.git
Cloning into 'gromacs'...
remote: Counting objects: 119131, done.
remote: Compressing objects: 100% (21428/21428), done.
remote: Total 119131 (delta 100642),
Hi Lara,
with the .mdp you sent you are NOT going to perform a minimization, but a NPT
equilibration run (i.e. a MD simulation, as stated in the first line). So check
a tutorial of your choice to get a proper .mdp for a simple energy minimization.
Greetings
Felix
-Ursprüngliche
On 6/29/12 6:27 AM, Michael Brunsteiner wrote:
hi
as suggested in: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
i do:
prompt git clone git://git.gromacs.org/gromacs.git
Cloning into 'gromacs'...
remote: Counting objects: 119131, done.
remote: Compressing objects: 100%
Hi
Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216
because this is what I am using with genbox. My mistake.
Now I used the equilibrating file out of this tutorial:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
I got the
On 6/29/12 8:04 AM, Lara Bunte wrote:
Hi
Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216
because this is what I am using with genbox. My mistake.
Now I used the equilibrating file out of this tutorial:
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I select the 13 (SOL)
Now I have in my topology file
[ molecules ]
; Compound#mols
HI , I have been performing SMD after reading bevan lab tutorial. The
tutorial was very informative in basic aspects. Now I have my ligand inside
the protein and I wan to pull it out in a specific direction. I applied
force separately along the X, Y and Z axis . In which none of the pull seems
to
Hi,
Check out the order of sections which you have included in your .top file. I
always got this error because of the wrong orders of sections.
Cheers,
Shima
From: reising...@rostlab.informatik.tu-muenchen.de
reising...@rostlab.informatik.tu-muenchen.de
On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I select the 13 (SOL)
Now I
On 6/29/12 9:04 AM, Shima Arasteh wrote:
Hi,
Check out the order of sections which you have included in your .top file. I
always got this error because of the wrong orders of sections.
Incorrect order will lead to a series of non-matching atom names in the grompp
output. In this case,
On 6/29/12 9:03 AM, Raj wrote:
HI , I have been performing SMD after reading bevan lab tutorial. The
tutorial was very informative in basic aspects. Now I have my ligand inside
the protein and I wan to pull it out in a specific direction. I applied
force separately along the X, Y and Z axis .
On 6/29/12 9:04 AM, massimo sandal wrote:
On 29 Jun 2012 14:08, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu
The settings in my tutorial are for use with OPLS-AA and are thus not
suitable for a simulation with CHARMM. Cutoffs and other aspects will be
different.
This is
So just entering the -pname NA and -nname CL !
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, June 29, 2012 5:36 PM
Subject: Re: [gmx-users] error with grompp
On 6/29/12
Hi Justin,
thank you for your answer.
So you mean that I should only name NA and CL like this:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA -nname CL
But when I now want to run the alraedy mentioned grompp command I get the
error:
No such
Thank you for your answer. I tried it only with NA and CL and it also
didn't work.
Now I have the same error with NA
Bests Eva
Hi,
Check out the order of sections which you have included in your .top file.
I always got this error because of the wrong orders of sections.
Cheers,
Shima
On 6/29/12 9:18 AM, Shima Arasteh wrote:
So just entering the -pname NA and -nname CL !
Precisely, as genion -h instructs.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
On 6/29/12 9:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
So you mean that I should only name NA and CL like this:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA -nname CL
This is a correct
Thanks for your reply Justin.
From your umbrella tutorial I thought the reference group should be the
protein. Now from your reply i think I can specify any amino acid residue in
the protein and I can drive the ligand towards the residue.
where I need to specify the group
If i'm using the pull
On 6/29/12 9:38 AM, Raj wrote:
Thanks for your reply Justin.
From your umbrella tutorial I thought the reference group should be the
protein. Now from your reply i think I can specify any amino acid residue in
the protein and I can drive the ligand towards the residue.
where I need to
You should have it. In CMakeLists.txt, PROJECT_VERSION should be set to
4.6-dev so you can check that.
ithat what i looks like ... i now get:
prompt mdrun_d
[...]
:-) VERSION 4.6-dev-20120629-9c6be1c (-:
[...]
which gives me:
g_bar_d -f mdv*.xvg -b 100
[...]
total 0.000 - 1.000, DG
On 6/29/12 11:08 AM, Michael Brunsteiner wrote:
You should have it. In CMakeLists.txt, PROJECT_VERSION should be set to
4.6-dev so you can check that.
ithat what i looks like ... i now get:
prompt mdrun_d
[...]
:-) VERSION 4.6-dev-20120629-9c6be1c (-:
[...]
which gives me:
g_bar_d -f
On 6/29/12 11:10 AM, massimo sandal wrote:
On 29 Jun 2012 15:09, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 6/29/12 9:04 AM, massimo sandal wrote:
On 29 Jun 2012 14:08, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu
Hi Steven,
How much is 1 [pN/A] in [kJ/nm2] (without the mol)?
And why would anyone want to use force-constants in the 10^-23 ?
So why not define a force-constant for 1 mol of bonds instead of a sole bond?
I think you can see where I'm going.
Oliver
On Fri, Jun 29, 2012 at 2:32 AM, Steven
Hi, I am trying to do polymer simulation with gromacs. I am new to
gromacs and trying to construct topology for a system of polymer
chains. My problem is that i am facing difficulties to creat pdb file
for polymer chain containing 1000 monomers. I have used PRODRG server
but it gives me a pdb and
Hi,
we've been trying to do free energy calculations for solvation of two
small molecules in water, n-butylamine (NBA) and diethyl-ether (DEE).
For one of them the result with BAR (using Justin's tutorial) is
significantly different from TI:
BAR TI Exper. (kJ/mol)
NBA -11.1
On 6/29/12 2:21 PM, Parvez khan wrote:
Hi, I am trying to do polymer simulation with gromacs. I am new to
gromacs and trying to construct topology for a system of polymer
chains. My problem is that i am facing difficulties to creat pdb file
for polymer chain containing 1000 monomers. I have
thanx a lot Justin for reply
Regards
parvez
On Fri, Jun 29, 2012 at 2:27 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/29/12 2:21 PM, Parvez khan wrote:
Hi, I am trying to do polymer simulation with gromacs. I am new to
gromacs and trying to construct topology for a system of polymer
Hello
My A.gro file is:
1PvB CB1 3.109 2.784 0.803 0. 0. 0.
1PvBHB12 3.156 2.880 0.843 0. 0. 0.
1PvBHB23 2.997 2.797 0.819 0. 0. 0.
1PvBHB34 3.129 2.765 0.693 0. 0. 0.
On 6/29/12 3:55 PM, sreeta.g wrote:
Hello
My A.gro file is:
1PvB CB1 3.109 2.784 0.803 0. 0. 0.
1PvBHB12 3.156 2.880 0.843 0. 0. 0.
1PvBHB23 2.997 2.797 0.819 0. 0. 0.
1PvBHB34
Hi Justin
Thank you for your reply.
However, when I am using the grompp command, the topol.tpr file is not being
formed due to a fatal error. This fatal error is the cumulative of ' No
default Ryckaert-Bell.' types for many atoms in the polymer chain.
Also, regarding the comment on the atom types
On 6/29/12 4:44 PM, sreeta.g wrote:
Hi Justin
Thank you for your reply.
However, when I am using the grompp command, the topol.tpr file is not being
formed due to a fatal error. This fatal error is the cumulative of ' No
default Ryckaert-Bell.' types for many atoms in the polymer chain.
And
Hi Justin,
yes I removed all the old resulting files and did everything again. So now
there is the topology and coordinate file with only NA and CL and not NA+
or CL-.
I also checked whether the molecules are listed in the same order as in
the .gro file and it is the case. So that is also
On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
yes I removed all the old resulting files and did everything again. So now
there is the topology and coordinate file with only NA and CL and not NA+
or CL-.
I also checked whether the molecules are listed in
Hi Justin
I have changed all the force field parameters as below, (I have already
shown my ffbonded.itp file)
ffnonbonded.itp
; name bond_typemasscharge ptype sigma epsilon
opls_966 CA612.01100 0.240 A3.5000e-01
3.3600e-01
opls_967 CA6
On 6/29/12 6:10 PM, sreeta.g wrote:
Hi Justin
I have changed all the force field parameters as below, (I have already
shown my ffbonded.itp file)
ffnonbonded.itp
; name bond_typemasscharge ptype sigma epsilon
opls_966 CA612.01100 0.240 A
Hi Justin
I read through the beastly error file and did as you said. It worked!
Just missed a few lines in the ffbonded.itp.
Thank you
--
View this message in context:
http://gromacs.5086.n6.nabble.com/top-file-incoherent-with-the-values-in-the-ffbonded-itp-file-tp4998966p4998975.html
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