Yes, it works (-chainsep interactive: merge = yes ) but when you process to
grompp there is an error:
Unknown cmap torsion between atoms 6002 6004 6006 6017 6021
pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with
first three residues of chain B. Removing these lines does
Hi all,
I am trying to get the electrostatic forces acting on each atom as a
function of time. I have checked the list and all the suggestions are
based on rerunning the simulation. Is there not an easy way to print
these forces on the fly ? If not, what is the cleanest way to remove
bonded a
Dear Gmx Users,
My system is made of 3 proteins. As I want to use distance restraints
dynamics between atoms belonging to each of them I have to produce topoloy
with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge:
yes).
Then when I process to grompp the error: "unknown cmap
On Thu, May 24, 2012 at 12:49 PM, wrote:
> Send gmx-users mailing list submissions to
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Dear all gromacs users,
While i am using the commond" pdb2gmx -f
4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and
errors.
Warning: Residue EME21 in chain has different type (Other) from starting
residue ALA1 (Protein).
Warning: Residue
Hello.
How to extract all low-energy conformations from MD-trajectory of protein?
--
Андрей Гончар
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On Thu, May 24, 2012 at 10:04 PM, Francesca wrote:
> I checked and the resul is the same...but now I know I can use -chainsep
> interactive!
>
>
Yes, it works (-chainsep interactive: merge = no ) but when you process to
grompp there is an error:
Unknown cmap torsion between atoms 6002 6004 6006 6
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Seera Suryanarayana [paluso...@gmail.com]
Sent: Friday, May 25, 2012 6:23 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error
Dear all gromacs users,
Hi Andrej,
You can use trjconv with -drop and -dropunder. Check trjconv -h.
Cheers,
Tsjerk
On Fri, May 25, 2012 at 11:03 AM, Андрей Гончар wrote:
> Hello.
> How to extract all low-energy conformations from MD-trajectory of protein?
>
> --
>
> Андрей Гончар
>
> --
> gmx-users mailing list gm
Dear??every one!
We found some problems of run gmx4.5.5 in parallel on the E3-1230 V2 CPU (Ivy
Bridge).
The compilers we used were ifort and icc (Version 12.0.3).
It only if the value of the option "-nt" > 2, the mdrun program crashed after
hundreds MD steps.
And we also noticed that the same .t
Hi,
I have a question regarding simulation of a protein-DNA-complex where
the protein encloses the DNA double helix. I did not find a tutorial for
a system of three rather big molecules like these, that's why I ask. If
there is such, I would appreciate a hint.
I want to start with a crystal
On 5/25/12 1:23 AM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am using the commond" pdb2gmx -f
4E82.pdb -o 4E82.gro -p 4E82.top".I am getting the following warnings and
errors.
Warning: Residue EME21 in chain has different type (Other) fr
can you write the atoms 6002 6004 6006 6017 6021 and all informations in your
topology file about these atoms??
Francesca
--
View this message in context:
http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997758.html
Sent from the GROMACS Users Forum mailing list archiv
On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote:
Hi all,
I am trying to get the electrostatic forces acting on each atom as a
function of time. I have checked the list and all the suggestions are
based on rerunning the simulation. Is there not an easy way to print
these forces on the fly ?
I think all the answers to your question are in the tutorial. Probably
read first the lysozyme tutorial and then the umbrella tutorial again.
But here is a more general answer:
Normally you have two types of simulations:
preperation (which is also equilibration)
production
and the need of rest
On 25/05/2012 7:52 PM, Steven Neumann wrote:
Dear Gmx Users,
My system is made of 3 proteins. As I want to use distance restraints
dynamics between atoms belonging to each of them I have to produce
topoloy with one moleculetype. I used pdb2gmx -chainsep interactive (I
used merge: yes).
Then
Dear Ahmed -
I do not understand how you imagine "FCC geometry" in the liquid state
of matter.
If you want to just resize my system, use the standard "genbox"
utility and then re-equilibrate at the desired temperature and density
(if you want to fix density, of course).
Dr. Vitaly V. Chaban, 43
Sure, possible.
But if you want to type the coordinates for FCC lattice using 500
atoms by hand, that's indeed cool.
On Fri, May 25, 2012 at 11:31 AM, ahmed sta wrote:
> I thought that it is possible to use text editor in order to fix the
> geometry, isn't it?
>
>
> ___
Hi,
Due to a mistake during commit cleanup we had to rewrite part of the
history of the nbnxn_hybrid_acc branch. As a consequence, pulling from
branches that track nbnxn_hybrid_acc will not work (it will result in
conflicts) and a forced update will be required:
$ git branch
nbnxn_hybrid_acc #
If you want a solid system, where atoms are arranged as in FCC, this
is another talk.
There two way to achieve your goal. Either --
1) you write a simple program which places argon atoms as in FCC.
OR
2) you try to freeze my system into your system using simulated
annealing implemented in groma
On Fri, May 25, 2012 at 4:15 PM, Francesca wrote:
> can you write the atoms 6002 6004 6006 6017 6021 and all informations in
> your
> topology file about these atoms??
>
> Francesca
>
Sure:
>From the begining:
Unknown cmap torsion between atoms 799 801 804 811 813
; residue 399 NON rtp NON q
Dear All
Although the tutorials on FE calculations are all excellent and useful, they
all appear to involve turning a molecule on or off. As I understand the
manual, it is also possible to change one atom into another, i.e. lambda=1
means 100% state A (and 0% state B) and lambda=0 means 100% stat
Writing your program has nothing to do with gromacs. If you do not
have experience in programming by far, it may be faster to use the
second route. But of you still want to generate a program yourself, I
am delighted to direct your attention to the PYTHON, python.org,
programming language.
I am aw
On Fri, May 25, 2012 at 4:18 PM, Mark Abraham wrote:
> On 25/05/2012 7:52 PM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> My system is made of 3 proteins. As I want to use distance restraints
>> dynamics between atoms belonging to each of them I have to produce topoloy
>> with one moleculetyp
probably means your trajectory is not continuous enough. I saw the same
thing when I try to "fit" an ensemble trajectory, which each frame is not
from the previous one. Or if your first frame in your trajectory is not
"good looking(or having good rmsd to your target structure)", fit option
cannot f
Hi Steven,
There will be three dihedrals spanning a break. Make sure to remove all of
them. Of course pdb2gmx shouldn't just connect the chain ends... Maybe you
can file it as a bug.
Cheers,
Tsjerk
On May 25, 2012 3:11 PM, "Steven Neumann" wrote:
Yes, it works (-chainsep interactive: merge =
if you create a bond you need to have angle, tortion etc...
Maybe when you processed pb2gmx it create a bond between the 799 and 801.
Francesca
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View this message in context:
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Sent from the GROMACS Users Foru
Ahmed -
This is *YOUR* research, not mine. I believe I have given you enough
hints to succeed.
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
On Fri, May 25, 2012 at 12:51 PM, ahmed sta
On 5/25/12 10:01 AM, Matthias Ernst wrote:
Hi,
I have a question regarding simulation of a protein-DNA-complex where the
protein encloses the DNA double helix. I did not find a tutorial for a system of
three rather big molecules like these, that's why I ask. If there is such, I
would appreciat
On 5/25/12 3:19 AM, rethina malliga wrote:
On 5/24/12 7:43 AM, rethina malliga wrote:
> Hi,
>
> I tried protein protein simulation in gromacs.
>
> I prepared one ptn and kept seperately with its .top, .itp, .gro files.
>
> Then I prepared another protein
On 5/25/12 5:52 AM, Steven Neumann wrote:
Dear Gmx Users,
My system is made of 3 proteins. As I want to use distance restraints dynamics
between atoms belonging to each of them I have to produce topoloy with one
moleculetype. I used pdb2gmx -chainsep interactive (I used merge: yes).
Then when
On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul wrote:
>
>
> On 5/25/12 5:52 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> My system is made of 3 proteins. As I want to use distance restraints
>> dynamics
>> between atoms belonging to each of them I have to produce topoloy with one
>> mo
Thanks Francesca. There is no bond between them. I merged topologies and
the grompp error comes from the gmx bug posted by Mark.
http://redmine.gromacs.org/issues/885
Thanks for this link Justin!
Steven
On Fri, May 25, 2012 at 5:47 PM, Francesca wrote:
> if you create a bond you need to have ang
On 5/25/12 5:04 PM, Steven Neumann wrote:
On Fri, May 25, 2012 at 2:34 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:
On 5/25/12 5:52 AM, Steven Neumann wrote:
Dear Gmx Users,
My system is made of 3 proteins. As I want to use distance restraints
dynamics
Dear Gmx Users,
My surface is made of 4 types of residues created on my own. They are
placed within they vdwradii away from each other. I want to keep the
surface rigid and allow it to move into only one direction (freezgrps,
freezdim). Each residue is made of one atom. The best option would be to
On 5/25/12 5:43 PM, Steven Neumann wrote:
Dear Gmx Users,
My surface is made of 4 types of residues created on my own. They are placed
within they vdwradii away from each other. I want to keep the surface rigid and
allow it to move into only one direction (freezgrps, freezdim). Each residue is
Hi All,
I have been using the PubChem database to search for uncharged small
molecules. However, even after specifying zero charge, PubChem still
outputs compounds containing amino groups (-NH2) and carboxylic acids
(-COOH); since I am interested in physiological pH, these compounds would
actuall
If there is tutorial for a system like yours it would probably have to be
(re)constructed from someone's publication. Multi-molecule systems shouldn't
be much different from your "typical" receptor-ligand system; if there isn't
a covalent bond between your dna and protein then life is even easier:
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