I am not going to compare this with anything , I have to look for sequences
and their corresponding energies and select the lowest scoring ones. I
request you to kindly elaborate on freezing some portion of the protein. (
I am bit confused as in my case I am fixing the dihedral of turn residues
whi
On 14/06/2012 4:38 PM, bharat gupta wrote:
Thanks Sir for the reply... This question is related to my first query
that if we constraint the dihedral of the turn residue how can we
fix/freeze the movement of other residues.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restra
Dear Gromacs Users!
I've forced with the problem durin insertion of my protein into
pre-equilibrated bilayer via G_Membed.
I've done all steps in accordance to the KALP tutorial ( I've oriented both
membrane as well as the protein in the same dimensions merged both
topologies and gro files in the
Thanks Sir for the reply... This question is related to my first query that
if we constraint the dihedral of the turn residue how can we fix/freeze the
movement of other residues. As I am interested in only getting the energy
of the hairpin when the turn residues are constrained within a particular
On 14/06/2012 3:56 PM, Tom Dupree wrote:
Greetings all,
I can't manually reproduce g_lie results.
After raging at excel for a while I think I have found a bug.
Here is my first time point,
Reported by g_lie to be 35.0073
> From energy file
Lj_complex =-130.762
Coul_complex = -286.746
My constant
Greetings all,
I can't manually reproduce g_lie results.
After raging at excel for a while I think I have found a bug.
Here is my first time point,
Reported by g_lie to be 35.0073
>From energy file
Lj_complex =-130.762
Coul_complex = -286.746
My constants specified to g_lie
Clj = Alpha = lj_const
On 14/06/2012 12:04 PM, bharat gupta wrote:
Thanks for the reply . Is it possible to calculate the dihedral energy
of certain residues, like in my case for turn residues ??.. How can
that be done
First, seek to define "dihedral energy"... Force fields are not
parametrized such that parts of t
Thanks for the reply . Is it possible to calculate the dihedral energy of
certain residues, like in my case for turn residues ??.. How can that be
done
This another question is regarding energy minimization. Suppose, I minimize
the the protein solvated in water, the energy value that I get is for
On 14/06/2012 11:42 AM, Christopher Neale wrote:
Dear users:
the gromacs web page directs me to http://redmine.gromacs.org/ to file
bug notifications.
The site, however, gives me a "500 internal server error".
Do I have the correct address?
Yes. It's down, and does so periodically.
Mark
--
On 6/13/12 9:44 PM, bharat gupta wrote:
Hi,
I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??
http://www.gromacs.org/Documentation/How-
On 6/13/12 9:42 PM, Christopher Neale wrote:
Dear users:
the gromacs web page directs me to http://redmine.gromacs.org/ to file bug
notifications.
The site, however, gives me a "500 internal server error".
Do I have the correct address?
That is the correct address. The page was down earli
Hi,
I wanted to simulate a beta-hairpin but with the dihedral angle of the turn
residues constrained as per my wish for eg phi angle should not 60 and psi
should be 90. Can anybody tell me how can I do this ??
Regards
--
Bharat
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.g
Dear users:
the gromacs web page directs me to http://redmine.gromacs.org/ to file bug
notifications.
The site, however, gives me a "500 internal server error".
Do I have the correct address?
Thank you,
Chris.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/
On 14/06/2012 2:31 AM, Anna Duncan wrote:
Hello all,
I'm doing a membrane-protein simulation using MARTINI of the ADP/ATP
carrier in a POPC/POPE membrane. After inserting the protein into the
membrane I solvated the system using g_genbox. In order to prevent
water beads from being placed
Hello all,
I'm doing a membrane-protein simulation using MARTINI of the ADP/ATP
carrier in a POPC/POPE membrane. After inserting the protein into the
membrane I solvated the system using g_genbox. In order to prevent
water beads from being placed within the bilayer, I made a local copy
Hi Justin,
Thanks. I will have a look at this link.
On Thu, Jun 14, 2012 at 12:27 AM, Justin A. Lemkul wrote:
>
>
> On 6/13/12 12:21 PM, Malai wrote:
>
>> Hi,
>>
>> Can you suggest me what went wrong in my production run . I got the
>> following
>> error that stopped my run. Thanks.
>>
>>
> htt
On 6/13/12 12:21 PM, Malai wrote:
Hi,
Can you suggest me what went wrong in my production run . I got the following
error that stopped my run. Thanks.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
---
Program mdrun
On 6/13/12 11:49 AM, ms wrote:
On 13/06/12 16:59, Justin A. Lemkul wrote:
On 6/13/12 10:48 AM, ms wrote:
On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
pr
Hi,
Can you suggest me what went wrong in my production run . I got the
following error that stopped my run. Thanks.
---
Program mdrun_mpi, VERSION 4.5.4
Source code file: domdec.c, line: 2861
Fatal error:
The X-size of the box (6.311743) times
On 13/06/12 16:59, Justin A. Lemkul wrote:
On 6/13/12 10:48 AM, ms wrote:
On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what
On 6/13/12 10:48 AM, ms wrote:
On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no
On 13/06/12 16:36, Justin A. Lemkul wrote:
Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some ins
On 6/13/12 10:20 AM, ms wrote:
Hi,
I am trying to prepare a simple system for tests with CUDA. My guinea pig is the
lysozyme system from this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
but I prepared it using the AMBER99sb-ildn f
Looking deeper, it seems most of the energy loss is concentrated in the
SR Coulomb interactions:
Energy Average Err.Est. RMSD Tot-Drift
---
Bond2771.28 17
Hi,
I am trying to prepare a simple system for tests with CUDA. My guinea
pig is the lysozyme system from this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
but I prepared it using the AMBER99sb-ildn force field and the SPCE
water m
On 6/13/12 9:22 AM, Malai wrote:
HI Justin,
I did use the .pdb file as I showed in the grompp command. If I got I/O error,
the mdrun should not work? but here the mdrun is working. Thanks.
As I said before, if the .tpr file was produced, there was no problem. The
error message makes no se
HI Justin,
I did use the .pdb file as I showed in the grompp command. If I got I/O
error, the mdrun should not work? but here the mdrun is working. Thanks.
On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul wrote:
>
>
> On 6/13/12 9:11 AM, Malai wrote:
>
>> Hello Justin,
>>
>> Thanks for reply.
On 6/13/12 9:11 AM, Malai wrote:
Hello Justin,
Thanks for reply. After getting this, I started to run production run but here i
didnt get any error. so is it OK? or still I need to look at this error? Thanks
What's anomalous to me is that grompp produced an I/O error (referencing an
unused
Hello Justin,
Thanks for reply. After getting this, I started to run production run but
here i didnt get any error. so is it OK? or still I need to look at this
error? Thanks
On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul wrote:
>
>
> On 6/13/12 8:27 AM, Malai wrote:
>
>> HI,
>>
>> Sorry for
On 6/13/12 8:59 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
I managed it with your help that the minimization run worked. Now I
prepared a .mdp file for the md run.
Can you please tell me if the following .mdp file is correct?
define = -DPOSRES
integrator
Hi Justin,
I managed it with your help that the minimization run worked. Now I
prepared a .mdp file for the md run.
Can you please tell me if the following .mdp file is correct?
define = -DPOSRES
integrator = md
constraints = all-bonds
emtol = 8
niter = 15
nsteps
On Wed, Jun 13, 2012 at 3:59 AM, Mark Abraham wrote:
> On 12/06/2012 10:49 PM, Ehud Schreiber wrote:
>
>> Message: 4
>>> Date: Mon, 11 Jun 2012 15:54:39 +1000
>>> From: Mark Abraham>
>>> Subject: Re: [gmx-users] GPU
>>> To: Discussion list for GROMACS users
>>> Message-ID:<4FD5881F.3040509@**anu.e
On 6/13/12 8:27 AM, Malai wrote:
HI,
Sorry for wrongly typing. The command I issued is: grompp -v -f hex1.mdp -c
hex1.pdb -p hex1.top -o hex1.tpr.
The error is bellow:
Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491
File input/output error:
hex1.gro
For more info
On 6/13/12 8:20 AM, delara aghaie wrote:
Dear Justin
If we do not get error when using command pdb2gmx, and so having the .top and
.gro files, Can we make sure that every thing is ok with our pdb file or maybe
there exists some other checks to be done on pdb?
If pdb2gmx produces no error, the
HI,
Sorry for wrongly typing. The command I issued is: grompp -v -f hex1.mdp
-c hex1.pdb -p hex1.top -o hex1.tpr.
The error is bellow:
Error:
Program grompp, VERSION 4.5.4
Source code file: futil.c, line: 491
File input/output error:
hex1.gro
For more information and tips for troubleshooting
Thank you very much for this quick answer!!
Eva
>
>
> On 6/13/12 7:55 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi!
>> Thank you for your answer.
>>
>>> On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de
>>> wrote:
Hi everybody,
I want to do a minimizati
On 6/13/12 7:55 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi!
Thank you for your answer.
On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.
Doesn't really mat
Hi!
Thank you for your answer.
> On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want to do a minimization of the hydrogens of my protein. Only the
>> hydrogens.
>
> Doesn't really matter - nothing will move more than a fraction of an
> Angstrom unl
On 6/13/12 7:48 AM, delara aghaie wrote:
Dear Justin
Thanks again for your response.
About renaming residue would you pls explain more? On which basis I should
select the new name?
The contents of the .pdb file and/or the RCSB website from which you downloaded
the file will tell you the exa
On 6/13/12 7:36 AM, Malai wrote:
Hi,
I used the command following to generate .tpr file for production but I got the
following error. Without considering this error, I run production but it is
working now. any problem will be in production?
The command below makes no sense; how is it that y
Hi,
I used the command following to generate .tpr file for production but I got
the following error. Without considering this error, I run production but
it is working now. any problem will be in production?
-v -f hex1.mpb -c hex1.pdb -p hex1.top -o hex1.pdb
Error:
Program grompp, VERSION 4.5.4
On 6/13/12 6:32 AM, delara aghaie wrote:
Dear Gromacs users
I want to create from 1AU1.pdb, the .gro and .top files.
Running this command
pdb2gmx -ignh -f 1AU1.pdb -o 1AU1.gro -p topo.top -water spce
and choose this forcefield:
GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
I get
Dear Gromacs users
I want to create from 1AU1.pdb, the .gro and .top files.
Running this command
pdb2gmx -ignh -f 1AU1.pdb -o 1AU1.gro -p topo.top -water spce
and choose this forcefield:
GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
I get this error:
Fatal error:
Residue 'BGC' not f
On 6/13/12 4:29 AM, Satish Kamath wrote:
Dear Sir,
I removed the H-H 1-4 interaction from pairs and this seems to have lowered
the potential a lot to 10^2 from 9000 but is still positive. But is it a
valid thing to do?
Haphazardly deleting energetic terms to produce a more desirable energy
>
> Dear Gromacs users
> I have encountered in pdb data bank with Human interferon crystal
> structure:
> PDB ID : 1ITF
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF
>
> It is mentioned that it contains 24 structures. I opened the file and
> saw there are 24 models there.
>
> Now
On 6/13/12 5:09 AM, Seera Suryanarayana wrote:
Dear all gromacs users,
I am doing moleculer dynamics by using gromacs software.I
got the following error after using the commond" mdrun -deffnm nvt".
Fatal error:
A charge group moved too far between two domain decompositio
Dear all gromacs users,
I am doing moleculer dynamics by using gromacs
software.I got the following error after using the commond" mdrun -deffnm
nvt".
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not w
On 13/06/2012 6:44 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.
Doesn't really matter - nothing will move more than a fraction of an
Angstrom unless it's horribly wrong, in which case not m
Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens. And I want to do this with implicit solvent.
All the time when I try it there are errors in my .mdp file. Can you
please give me an example how such a .mdp file should look like.
Thank you,
Eva
--
gmx-u
> On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi,
>> I want to do a MD simulation in vacuum.
>
> So don't turn on implicit solvent.
Sorry,
my fault. I want to do it in implicit solvent.
>
>> So first I wanted to prepare the
>> files for that with "grompp".
>> But
Dear Sir,
I removed the H-H 1-4 interaction from pairs and this seems to have lowered
the potential a lot to 10^2 from 9000 but is still positive. But is it a
valid thing to do?
Satish Kamath
IISc Bangalore
India
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Positive-Poten
On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
I want to do a MD simulation in vacuum.
So don't turn on implicit solvent.
So first I wanted to prepare the
files for that with "grompp".
But there I got the error that
"With GBSA implicit solvent, rgbradii must
Hi,
I want to do a MD simulation in vacuum. So first I wanted to prepare the
files for that with "grompp".
But there I got the error that
"With GBSA implicit solvent, rgbradii must be equal to rlist"
But the 2 values are the same in my .mdp file. Can you please show me
where the failure is?
defi
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