Dear gmx-users,
I am currently trying to simulate a thermalized wall of coarse-grained
particles. I model the wall in the framework of the bead on spring approach.
The wall molecules are defined as dimers :
[ moleculetype ]
; molname nrexcl
ROCK1
[ atoms ]
;id type
I suppose by "full body dock" you mean rigid body docking, correct me if I
am wrong. In that case you could create initial starting structure for
flexible peptide docking. Rosetta accepts even coarse-grained models, namely
only the backbone, and then builds the full-atom structures.
Alternatively
Hi Liao,
Your python installation seems to be missing the datetime module, which is
very bizarre. Please verify your Python installation, you may have issues
with your PYTHONPATH.
Regards,
Alan
2011/4/12 fancy2012
> Hi GMX users,
> When I ran acpype.py on my computer, I got one error like th
CABS is able to conduct blind docking of peptides. You may also use the
predicted poses as starting structures for the Rosetta. Have a look at this:
http://www.springerlink.com/content/p6223376886054m6/
On 12 April 2011 10:22, Thomas Evangelidis wrote:
> I suppose by "full body dock" you mean
Interesting. I can't see why that wouldn't be possible in theory, but
there is a part of the code that would need rewriting, however.
Erik
Nilesh Dhumal skrev 2011-04-12 04.11:
I tried to use contact and -da together with following command
g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc
Hi Mark,
Thank you for your reply. But, I couldn’t understand very well what you
meant “you can make one that uses backbone-style linking. Most of the
forcefields will have examples of non-amino-acid terminating residues -
these make a single peptide bond just like yours does.”. So, let me explai
China)
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On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
Hi Mark,
Thank you for your reply. But, I couldn’t understand very well what
you meant “you can make one that uses backbone-style linking. Most of
the forcefields will have examples of non-amino-acid terminating
residues - these make a single
nts.
>
> Yours sincerely,
> Chaofu Wu, Dr.
>--
>Department of Chemistry and Materials Science, Hunan University of
> Humanities, Science and Technology, Loudi 417000, the People?s
> Republic of China (P.R. China)
> -- next part
thanks Mark and Tsjerk
i got it..!
--- On Mon, 4/11/11, Tsjerk Wassenaar wrote:
From: Tsjerk Wassenaar
Subject: Re: [gmx-users] orientational relaxation
To: "Discussion list for GROMACS users"
Date: Monday, April 11, 2011, 10:54 PM
Hi Daniel,
If you want to fix the com position, specify the
First of all, I don't know
if this is the right forum to
discuss issues related to acpype. You should try to
contact the acpype team.
I'm not an acpype expert but if I
can help you, do not hesitate to contact
me through my email.
Some tips:
Considering that python, openbabel and Ambertools
Miguel Quiliano Meza wrote:
Dear community.
Justin was right.
I did not want to make the explanation so long, but you're right I have
to put those details. As you will see I had to redirect the "outputs"
after perform "*./configure*" and "*make*" (these files are attach to
this mail).
I
You should check also that you use for acpype a python installation
under which the openbabel is installed.
Lucio Montero
Instituto de Biotecnología, UNAM.
---
El mar, 12-04-2011 a las 07:29 -0700, Aldo Segura escribió:
> First of all, I don't kn
Hi,
I've started using version 4.5.4 of gromacs, having previously been
using version 4.0 on an older server.
When I run a simulation on v4.0 everything seems to run fine.
However, when I run the same simulation on v4.5.4, mdrun gives me the
error message:
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Hi everyone.
I followed the steps in
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites for
my problem, but I obtained problems at the moment to perform "make".
So, as mention the web page of gromacs...
If you get errors during GROMACS compilation (the "make" step) that sug
Miguel Quiliano Meza wrote:
Hi everyone.
I followed the steps in
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites
for my problem, but I obtained problems at the moment to perform "make".
So, as mention the web page of gromacs...
If you get errors during GROMACS com
Hi,
I am running essential dynamics for a protein in water system (charmm-nocmap
and tip3p). I use the first 25 eigenvectors and targeted ED. It stops after
630ps when settle and lincs start giving warnings.
Step 315573, time 631.146 (ps) LINCS WARNING
relative constraint deviation after LINCS:
Hello
I am trying to build a solvent box of two solvents. Water & octane.
I want to create a interface at a particular site of the protein, as i am
studying interfacial activation of Lipase's lid.
Kindly suggest.
Thanks
Yuvraj
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.groma
On 13/04/2011 7:09 AM, YUVRAJ UBOVEJA wrote:
Hello
I am trying to build a solvent box of two solvents. Water & octane.
I want to create a interface at a particular site of the protein, as i
am studying interfacial activation of Lipase's lid.
Kindly suggest.
The mailing list archives contain
Mark Abraham wrote:
On 13/04/2011 7:09 AM, YUVRAJ UBOVEJA wrote:
Hello
I am trying to build a solvent box of two solvents. Water & octane.
I want to create a interface at a particular site of the protein, as i
am studying interfacial activation of Lipase's lid.
Kindly suggest.
The mailing
Please make sure to keep all discussion on the list.
Miguel Quiliano Meza wrote:
Hi Justin.
Unfortunately, the problem persist. So... for the moment I had to
Well, unless you can provide exact input (commands) and output (error messages)
for what you're doing, you're going to stay stuck, u
On 13/04/2011 2:10 AM, Anna Duncan wrote:
Hi,
I've started using version 4.5.4 of gromacs, having previously been
using version 4.0 on an older server.
When I run a simulation on v4.0 everything seems to run fine.
However, when I run the same simulation on v4.5.4, mdrun gives me the
error
On 13/04/2011 3:38 AM, Miguel Quiliano Meza wrote:
Hi everyone.
I followed the steps in
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites
for my problem, but I obtained problems at the moment to perform "make".
So, as mention the web page of gromacs...
If you get erro
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