[ccp4bb] Summary: MD program suitable to compute trajectories of a very small molecule in a protein

[Fred Vellieux]

Dear all,

Thank you for your help.

Here is a summary of the replies received:

---> Neli Fonseca, EBI, suggested the use of Docker containers,
"
https://hub.docker.com/search?q=gromacs=image

https://hub.docker.com/search?q=cp2k=image

https://hub.docker.com/search?q=nwchem=image "

---> Jeroen Mesters, Biochem Uni Lubeck and later Amit Singh pointed at 
the pkgs page for gromacs (Centos 7):


https://centos.pkgs.org/7/epel-x86_64/gromacs-2018.8-1.el7.x86_64.rpm.html

It then became clear why my attempt at "yum install gromacs" followed by 
"which gromacs" returned an error message (the command is "gmx");


---> Chris Roome, mpimf-heidelberg:
"If you're insterested, recently compiled the latest Gromacs 2020, seems 
to work fine.


I compiled GCC v5.5.0 first, and set the LD... and exe path (your path 
will differ of course) here's mine, with tcsh:


setenv LD_LIBRARY_PATH /software/gcc-5/lib64
set path = ( /software/gcc-5/bin $path )

As you say, even with this, cmake picks up the old, system installed 
gcc, so I had to specify on the cmake cmd:


cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON 
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=c++ -DGMX_MPI=on 
-DCMAKE_INSTALL_PREFIX=/software/gromacs-2020 -DREGRESSIONTEST_DOWNLOAD


since cmake picks up the old cc even with the correct paths.

I installed the MPI version, so if you want that, you'll need to install 
the openmpi and openmpi-devel packages with yum. Then do a 'module load 
mpi' before the cmake."


--->  Abhik Mukhopadhyay suggested the use of NAMD, 
https://www.ks.uiuc.edu/Research/namd/


---> Eugene Osipov: you can try NAMD, Amber (cost-free CPU-only academic 
version) or Desmond - their installation is simple and they work 
reasonably well.


---> Jack Tanner (U. Missouri-Columbia): "You might want to review the 
literature on using MD to study diffusion of O2/CO in myoglobin." (I had 
started in fact)


[---> Lorenzo Briganti: the reply seems to have been lost along the way].

Hoping this will be useful to others, and thank you once again.

Fred. Vellieux, 1st Faculty of Medicine, Charles University in Prague, 
BIOCEV Vestec site




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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Workshop – Specimen Preparation and Data Collection

[Dunn, Lisa B.]

S2C2 Workshop – Cryo-EM Specimen Preparation and Data Collection, March 23-25, 
2020

Stanford-SLAC Cryo-EM Center (S2C2) will offer a beginning cryo-EM training 
workshop held at SLAC National Accelerator Laboratory between March 23 and 25, 
2020.  Onsite attendance for the lecture sessions is limited to ~40 
participants with additional access provided via Zoom teleconferencing.  The 
hands-on sessions are limited to 12 participants.  There is no fee for this 
workshop.  If you are interested, you may apply by March 15, 2020 at:   
https://cryoem.slac.stanford.edu/s2c2/training/s2c2-workshops/next-workshop

Day 1: March 23, 2020
Wah Chiu : TEM basics and radiation damage
Robert M. Glaeser : Challenges in cryo-specimen preparation, and principles 
of image phase contrast and phase plate
Christopher Booth : Principles and operation of direct detector and energy 
filter
Yee Ting Li : CryoEM elogbook; data management and image quality assessment 
during data collection
Yifan Cheng : Best practices in cryoEM: what to do and not to do in 
tackling a new specimen

Day 2: March 24, 2020
Brenda Gonzalez and Ziwei Huang : Using virtual reality for training in 
cryo-specimen preparation for cryoEM
Practical sessions in small groups for cryo-specimen preparation and cryoEM 
operation

Day 3: March 25, 2020
Practical sessions in small groups for cryo-specimen preparation and cryoEM 
operation

We look forward to providing this training in March!

The Organizers

Corey Hecksel
heck...@stanford.edu

Michael Schmid
mfsch...@stanford.edu

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] Postdoctoral position at Cedars-Sinai, Los Angeles

[Avradip Chatterjee]

The Murali Lab at Cedars-Sinai Medical Center, Los Angeles, is seeking a 
Postdoctoral scientist trained in X-ray crystallography. 

 

The laboratory focuses on a number of immune and oncology-based protein targets 
and is equipped with an array of instruments including a Rigaku MicroMax 007-HF 
X-ray generator/RAXIS IV++ detector, SensiQ Pioneer SPR system, NanoTemper 
Microscale Thermophoresis and Art Robbins Gryphon and Scorpion robotics. More 
details about the laboratory can be found at: 
http://cedars-sinai.edu/Research/Research-Labs/Murali-Lab/index.aspx

 

Suitable candidates would possess two or more of the following skills:

1) Extensive experience in bacterial and/or insect cell expression/purification

2) Extensive experience with FPLC and HPLC for protein 
purification/characterization

3) Some experience using SPR and/or Microscale Thermophoresis technique for 
analyzing both protein-protein and protein-small molecule interactions

4) Experience in protein crystallization and structure determination by X-ray 
crystallography and experience in synchrotron-based structure biology 
experiments.

 

Interested candidates need to apply through the following web page:

https://jobs.cedars-sinai.edu/job/los-angeles/research-postdoctoral-scientist-murali-lab-structural-biology-and-molecular-therapeutics/252/14588858

 
Informal enquiries are welcome and should be directed to 
ramachandran.mur...@csmc.edu.



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[ccp4bb] SFX PostDoc position available at ASU, Tempe, Arizona

[Sabine BOTHA]

Dear all,

We still have a PostDoc position available for an exceptional candidate with 
experience in crystallography (or a skilled programmer willing to learn 
crystallography) to join our serial crystallography data analysis team at 
Arizona State University! 

The successful candidate will have the opportunity to become part of the 
BioXFEL Science and Technology Center (composed of 8 U.S. research 
universities) and its vast network of leading scientists. 
Our group at ASU develops tools for data processing of serial crystallographic 
data (from small molecules through MOFs to multi-domain membrane proteins), as 
well as assisting with beamtime experiments at synchrotrons and free electron 
lasers around the world. ASU ranks #1 in the U.S. for innovation, and we are 
currently in the process of commissioning the first pulsed X-ray source in the 
world. Furthermore, the weather in Arizona is always fantastic!

For more information please see the job posting at 
https://apply.interfolio.com/69791  or 
contact John Spence, john.spe...@asu.edu 

To apply, please send electronically to  http://apply.interfolio.com/69791 
 the following materials:  (a) a cover 
letter, (b) a CV, (c) a publication list, (d) a detailed summary of research 
experience and interests, and (e) 3 reference letters. 

Kind regards,
Sabine Botha


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Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Amit Singh]

Dear Fred,

Please follow the instructions below to install Gromacs on your CentOS
system without any other prerequisite.

https://centos.pkgs.org/7/epel-x86_64/gromacs-2018.8-1.el7.x86_64.rpm.html


On Thu, 23 Jan, 2020, 4:51 pm Tanner, John J., 
wrote:

> Fred,
>
> You might want to review the literature on using MD to study diffusion of
> O2/CO in myoglobin.
>
> Jack
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Associate Chair of Biochemistry
> Department of Biochemistry
> University of Missouri
> 117 Schweitzer Hall
> 503 S College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Email: tanne...@missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
> On Jan 23, 2020, at 3:43 AM, Fred Vellieux 
> wrote:
>
> Dear all,
>
> I need to run MD calculations in order to follow the trajectories of a
> very small molecule inside a protein. From previous calculations (not MD) I
> have starting positions for this small molecule that all seem in agreement
> with a possible path of motion inside the protein.
>
> Now I need to access a MD program (without licensing costs).
>
> I've had a look at the software list provided in Wikipedia (and tried to
> install the software, in succession, alas without success):
>
> cp2k - present for CentOS6 (with yum install ?) but appears to have
> vanished for CentOS7;
>
> gromacs requires a gcc version I don't have (even after having compiled
> and installed a suitable gcc version, cmake complains about the "old
> version" and stops);
>
> NWChem is unhappy with the Python setup and doesn't compile.
>
> I don't know how to solve all these OS version, library, unsuitable binary
> etc problems. In fact I don't know if any of these 3 software suites would
> be suitable for what I have in mind.
>
> Hence would anyone know of a useful MD software suite that would be
> suitable for my purpose and comes with statically linked binaries suitable
> for Intel 64 (Linux) ? Just launch the executable and it runs, no questions
> asked...
>
> Thank you,
>
> Fred.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
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Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Tanner, John J.]

Fred,

You might want to review the literature on using MD to study diffusion of O2/CO 
in myoglobin.

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jan 23, 2020, at 3:43 AM, Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:

Dear all,

I need to run MD calculations in order to follow the trajectories of a very 
small molecule inside a protein. From previous calculations (not MD) I have 
starting positions for this small molecule that all seem in agreement with a 
possible path of motion inside the protein.

Now I need to access a MD program (without licensing costs).

I've had a look at the software list provided in Wikipedia (and tried to 
install the software, in succession, alas without success):

cp2k - present for CentOS6 (with yum install ?) but appears to have vanished 
for CentOS7;

gromacs requires a gcc version I don't have (even after having compiled and 
installed a suitable gcc version, cmake complains about the "old version" and 
stops);

NWChem is unhappy with the Python setup and doesn't compile.

I don't know how to solve all these OS version, library, unsuitable binary etc 
problems. In fact I don't know if any of these 3 software suites would be 
suitable for what I have in mind.

Hence would anyone know of a useful MD software suite that would be suitable 
for my purpose and comes with statically linked binaries suitable for Intel 64 
(Linux) ? Just launch the executable and it runs, no questions asked...

Thank you,

Fred.



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[ccp4bb] Postdoc opportunities (Cambridge, UK)

[Yorgo Modis]

Dear CCP4BB,

The group of Yorgo Modis (University of Cambridge) has two funded postdoc 
positions available to study how cells sense and silence viral RNA and DNA. The 
group benefits from an outstanding environment in the Department of Medicine’s 
Molecular Immunity Unit, which is embedded within the MRC Laboratory of 
Molecular Biology (MRC-LMB). The group uses a combination of X-ray 
crystallography, cryoEM, biochemical assays, proteomics and cell-based 
signaling assays. 

Informal enquiries are welcome. Please spread the word or apply here: 
http://www.jobs.cam.ac.uk/job/24736/  
(closing date: 9th February)

Sincerely,

Yorgo Modis

___
Yorgo Modis, Ph.D.  Phone: 
+44/0 1223 267282
Reader in Virology and Immunology
Wellcome Trust Senior Research Fellow
Department of Medicine
University of Cambridge
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge, CB2 0QH, UK




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[ccp4bb] Job: PDRA crystallography drug discovery protein production

[Chris Dowson]

Full time, fixed term contract until 31 December 2021.

https://www.jobs.ac.uk/job/BXB907/research-fellow-78236-119

Funding at level 6 is available for a maximum 18 months restricted to end by 31 
December 21

CHNUK: Structural approaches to novel fragment based and natural product 
antibiotic discovery

Applications are invited for a highly motivated and experienced postdoctoral 
researcher to join an active research group at the School of Life Sciences, 
University of Warwick supervised by a team headed by Prof Chris Dowson. The 
project, which has been recently funded by the Newton Fund, focuses on 
acquiring specific structural and biochemical data using a novel strategy of HT 
affinity crystallography, using robust crystals of well validated and novel 
antibacterial targets to identify either fragment-based inhibitors or 
inhibitors identified by crystallography directly from complex mixtures of 
natural products. This position is available for up to 18 months in the first 
instance and will involve substantive interactions with academic colleagues at 
Harwell (Prof Frank vonDelft) and those in China at the Shanghai synchrotron.

You will have a PhD in a relevant field. The successful applicant should have 
proficiency in molecular cloning, protein expression, purification, 
crystallization, X-ray crystal structure determination in particular and should 
have a background in biochemistry or molecular biology/ drug discovery 
generally.

The School of Life Sciences at Warwick is equipped with state-of-the-art 
protein expression and purification apparatus, including high-throughput 
facilities for crystallisation and visualisation as well as regular synchrotron 
access in the UK and abroad. The wider laboratory is very well equipped with 
microbiological, biochemical and biophysical infrastructure and the successful 
applicant will join a wider team of highly motivated scientists working on a 
range of antimicrobial discovery and resistance projects.

Email: c.g.dow...@warwick.ac.uk

Website: https://warwick.ac.uk/fac/sci/lifesci/research/infdisease.

Closing date: 31 January 2020

Full details of the duties and selection criteria for this role can be found in 
the vacancy advert on the University of Warwick’s jobs pages. You will be 
routed to this when you click on the Apply button below.



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Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Abhik Mukhopadhyay]

Dear Fred,
Have you tried NAMD

https://www.ks.uiuc.edu/Research/namd/

Abhik


On Thu, Jan 23, 2020 at 9:43 AM Fred Vellieux 
wrote:

> Dear all,
>
> I need to run MD calculations in order to follow the trajectories of a
> very small molecule inside a protein. From previous calculations (not
> MD) I have starting positions for this small molecule that all seem in
> agreement with a possible path of motion inside the protein.
>
> Now I need to access a MD program (without licensing costs).
>
> I've had a look at the software list provided in Wikipedia (and tried to
> install the software, in succession, alas without success):
>
> cp2k - present for CentOS6 (with yum install ?) but appears to have
> vanished for CentOS7;
>
> gromacs requires a gcc version I don't have (even after having compiled
> and installed a suitable gcc version, cmake complains about the "old
> version" and stops);
>
> NWChem is unhappy with the Python setup and doesn't compile.
>
> I don't know how to solve all these OS version, library, unsuitable
> binary etc problems. In fact I don't know if any of these 3 software
> suites would be suitable for what I have in mind.
>
> Hence would anyone know of a useful MD software suite that would be
> suitable for my purpose and comes with statically linked binaries
> suitable for Intel 64 (Linux) ? Just launch the executable and it runs,
> no questions asked...
>
> Thank you,
>
> Fred.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Fred Vellieux]

Dear all,

I need to run MD calculations in order to follow the trajectories of a 
very small molecule inside a protein. From previous calculations (not 
MD) I have starting positions for this small molecule that all seem in 
agreement with a possible path of motion inside the protein.


Now I need to access a MD program (without licensing costs).

I've had a look at the software list provided in Wikipedia (and tried to 
install the software, in succession, alas without success):


cp2k - present for CentOS6 (with yum install ?) but appears to have 
vanished for CentOS7;


gromacs requires a gcc version I don't have (even after having compiled 
and installed a suitable gcc version, cmake complains about the "old 
version" and stops);


NWChem is unhappy with the Python setup and doesn't compile.

I don't know how to solve all these OS version, library, unsuitable 
binary etc problems. In fact I don't know if any of these 3 software 
suites would be suitable for what I have in mind.


Hence would anyone know of a useful MD software suite that would be 
suitable for my purpose and comes with statically linked binaries 
suitable for Intel 64 (Linux) ? Just launch the executable and it runs, 
no questions asked...


Thank you,

Fred.



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