My suggestion is to either add the ligand back in after g_membed removes it
or to not g_membed the system with the ligand, if it is acceptable. (Is your
ligand supposed to interact with the bilayer in any meaningful way?)
Or don't use g_membed and fall back to inflatgro for insertion.
On 2012-06
Yes, meant that file (didn't know the name for GMX 4.5.x, i use mainly
4.0.7).
You can use:
editconf -f *.pdb -o *.gro
to convert the *.pdb file into a *.gro file. Since the *.gro file has
only informations about:
atom names
residue name
coordinates
while the *.pdb has also additional informat
On 6/20/12 12:13 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
With the *nb.itp file you ment the "ffnonbonded.itp" file, right?
Yes. Thomas was referring to the old nomenclature of force field files.
But there is one thing:
Of course you are right, I can modify the .top file an
With the *nb.itp file you ment the "ffnonbonded.itp" file, right?
But there is one thing:
Of course you are right, I can modify the .top file and add my Dummy atom
there. But because I got this error I mentioned, the pdb2gmx didn't
produce a .gro file.
Bests, Eva
> 'pdb2gmx' is mainly a tool to
Thank you very much for this detailed answer!!
> 'pdb2gmx' is mainly a tool to get the topology for (bigger) molecules
> from a *.pdb file. 'pdbgmx' is expecting an entry in the *.rtp file for
> the dummy atoms. You could add one in that file... (see further below)
>
> But if the dummys only inter
'pdb2gmx' is mainly a tool to get the topology for (bigger) molecules
from a *.pdb file. 'pdbgmx' is expecting an entry in the *.rtp file for
the dummy atoms. You could add one in that file... (see further below)
But if the dummys only interact via nonbonded interactions it would be
more convi
On 6/20/12 11:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
yes I have already seen this site, but want I meant is that I have no idea
which values I should set. Is there something like a standard for dummy
protein for membrane?
No. You have to decide what these dummy
Hi Justin,
yes I have already seen this site, but want I meant is that I have no idea
which values I should set. Is there something like a standard for dummy
protein for membrane?
Eva
>
>
> On 6/20/12 10:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>>
>> I try to use
On 6/20/12 10:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I try to use GROMACS for my protein where I added a layer of dummy atoms
simulating the membrane around it.
But now when I want to call "pdb2gmx" I always get the error:
Fatal error:
Residue 'DUM' not found
Hi everybody,
I try to use GROMACS for my protein where I added a layer of dummy atoms
simulating the membrane around it.
But now when I want to call "pdb2gmx" I always get the error:
Fatal error:
Residue 'DUM' not found in residue topology database
I understand the error, that there is no entry f
Allowed the use of force field OPLS-AA in
GPU-GROMACS (GROMACS v.4.5.3 или GROMACS v.4.5.5) ?
Video Card: nVidia GeForce GTS 450
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Allowed the use of force field OPLS-AA in
GPU-GROMACS (GROMACS v.4.5.3 или GROMACS v.4.5.5) ?
Video Card: nVidia GeForce GTS 450
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Sent from the GROMACS Users Forum mailing list archive at Na
Dear Abraham,
I can do it now.
Thanks,
Son Tung.
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gmx-users mailing listgmx-use
Hi Justin,
okey, thanks for your answer. I will try to find out were I overwrite
those groups.
Eva
>
>
> On 6/20/12 4:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I wanted to fix the whole protein with "genrestr" so that only the water
>> molecules are flexible. I
On 6/20/12 7:10 AM, ankita oindrila wrote:
I am doing simulation of membrane protein in lipid bi layer for my
college project!.
can you please elaborate on the shrinking step that needs to be
iterated to get the right protein per lipid area.
You will have to be more specific about what y
On 6/20/12 4:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I wanted to fix the whole protein with "genrestr" so that only the water
molecules are flexible. I already did this once and there I had about 13
options what I want to fix so that I could select "protein"
But
I am doing simulation of membrane protein in lipid bi layer for my
college project!.
can you please elaborate on the shrinking step that needs to be
iterated to get the right protein per lipid area.
thanks.
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On 20/06/2012 8:34 PM, Son Tung Ngo wrote:
Dear Dr. Lemkul,
Many thanks for your reply. Would you like to explain for me how I can use
single-atom charge groups in gromacs simulation, please?
Search for charge groups in chapter 5 of the manual.
Mark
--
gmx-users mailing listgmx-users@grom
Dear Dr. Lemkul,
Many thanks for your reply. Would you like to explain for me how I can use
single-atom charge groups in gromacs simulation, please?
Regards,
Son Tung Ngo.
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From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Marzinek, Jan [j.marzine...@imperial.ac.uk]
Sent: Wednesday, June 20, 2012 10:30 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraints
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Anik Sen [anik...@csmcri.org]
Sent: Wednesday, June 20, 2012 10:20 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraints
Dear Mark,
In
Dear Mark,
i GOT IT. I understood my mistake and now it is running. Thanx for your help.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Anik Sen [anik...@csmcri.org]
Sent: Wednesday, June 20, 2012 2:50 PM
To: Discussion l
Dear Mark,
In the section it is written that :
" freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z
position will not be updated; e.g. Lipid SOL). freezedim specifies for which
dimension the freezing applies. To avoid spurious contibrutions to the virial
and pressure due
Hi everybody,
I wanted to fix the whole protein with "genrestr" so that only the water
molecules are flexible. I already did this once and there I had about 13
options what I want to fix so that I could select "protein"
But now I only have 3 options what I can fix: System, Water, SOL.
The only diff
Dear Gromacs users!
I'm simulatting membrane receptor in the explicit membrane surrounded by
water. Durring this MD run I've noticed that individual waters move into
the receptor interiour from the surroundings leaflets ( In my case mainly
from upper leaflet). How I could examine dynamics of such
But where exactly error in such inclussion ?
In G_membed manual I've found only this statement about inclussion of the
ligands
When the group to embed is not a default group, such as a protein and
its crystal water, an ndx file
should also be provided to g membed. Make sure all the molecule t
On 20/06/2012 5:08 PM, James Starlight wrote:
Mark,
I've made changes in the input mdp file
integrator = md
energygrps = Protein_ADN
freezegrps = Protein_ADN
freezedim = Y Y Y
energygrp_table
energygrp_excl = Protein_ADN Protein_ADN
here Protein_ADN is the protein_ligand defi
On 20/06/2012 5:24 PM, Anik Sen wrote:
Hello Justin
For freezefprs, am using the .mdp file as follows:
; title = NACL6
cpp = /usr/bin/cpp
define = -DPOSRE
constraints = none
integrator = steep
freezegrps = K+ CL-
freezed
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Anik Sen [anik...@csmcri.org]
Sent: Wednesday, June 20, 2012 8:24 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraint
Hello Justin
For freezefprs, am using the .mdp file as follows:
; title = NACL6
cpp = /usr/bin/cpp
define = -DPOSRE
constraints = none
integrator = steep
freezegrps = K+ CL-
freezedim = N N
.
Mark,
I've made changes in the input mdp file
integrator = md
energygrps = Protein_ADN
freezegrps = Protein_ADN
freezedim = Y Y Y
energygrp_table
energygrp_excl = Protein_ADN Protein_ADN
here Protein_ADN is the protein_ligand defined in the index.mdp
than I've processed by gro
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