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

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

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

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 lim

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

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

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

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

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

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 li

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

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

[ccp4bb] Postdoc opportunities (Cambridge, UK)

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

[ccp4bb] Job: PDRA crystallography drug discovery protein production

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 dis

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

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)

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

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 nee