Blog Archives

How to restart a Glide job that crashed

10/31/2012

While running, Glide saves the output in a temporary directory. The location of the temporary directory is found in the .file that is being stored in the directory from where you launched the job. Usually it is in /scratch.
In the temporary directory you should locate and save the _raw.maegz file which contains the Glide results up to the point when your job crashed. Then, open the .log file and see what is the ligand number when your job stopped. Rename the .in file and open it. Change the LIGAND_START parameter to the ligand number that you experienced the crash.

Another way to recover the job is to list the active (and unfinished) jobs with "jobcontrol".
As mentioned in the jobcontrol manual you can type
"$SCHRODINGER/jobcontrol -list" to list all the active jobs and
"$SCHRODINGER/jobcontrol -recover <jobid>" to recover your job, which means that the _raw.maegz file will be simply copied in the original working directory.

The last option, which I have not tried is to restart the Glide job with the
"$SCHRODINGER/glide -restart" option, which however works only for distributed glide jobs (as mentioned in the manual).

Zoe

Rosetta in the Amazon cloud

10/30/2012

Rosetta@cloud is hosted on Amazon’s Elastic Computing Cloud (EC2) which is part of Amazon Web Services (AWS) and Rosetta@cloud billing is done through Amazon’s DevPay system. You don't need to have your own cluster anymore, just buy time at AWS. To obtain an AWS account you will need a credit card which Rosetta@cloud services will be charged and you will need to do an automated telephone identity verification.

AWS has lots of commercial and free HPC molecular modeling suites such as NAMD, Schrodinger, etc.

Zoe

Molecular Dynamics benchmark reports from NVIDIA

10/30/2012

New Molecular Dynamics Benchmark Reports – Oct 2012 are now available from NVIDIA:

Download Benchmark Reports at www.nvidia.com/GPUTestDrive

AMBER, GROMACS, LAMMPS, NAMD reports provide:
a. Benchmark data on latest GPU architectures
b. Hardware recommendations

Free tests of your GPU code can be performed on NVIDIA's remotely-hosted cluster.

Zoe

Maestro Quick Reference Card

10/30/2012

Here you can download a reference card for common operations and shortcuts in Maestro 9.3.

Eva

LOLIPOP: a tool to identify the pi-stacking ability of (poly)aromatic rings.

10/29/2012

LOLIPOP was published in Chem. Comm. 2012.

You can find download instructions for LOLIPOP here.

Harris

Top Companies for Chemists

10/24/2012

Excerpt from the C&EN magazine of the American Chemical Society:

"Gone are the days when a chemist could be strictly a chemist. Today’s interdisciplinary world often requires a chemist to also don the hat of biologist, computer scientist, engineer, or medical researcher. The four companies highlighted in this year’s C&EN profile of top companies to work for relish these shifting boundaries. They’ve discovered that giving employees room to grow into their unique talents and interests benefits the company as a whole."

Find out what are the top 20 companies to work as a chemist here.

Zoe

32bit program compatibility with 64bit computers

10/24/2012

If you are trying to run a program and get the error message:
"File not found"
while your program is really there and it is not missing, then your problem might be that you are trying to run a 32-bit executable on a 64-bit computer.

The solution is to install the ia32-libs package for backwards 32bit compatibility. Run:

1) dpkg -s ia32-libs ; to check whether the ia32-libs package is installed or not
2) open "Ubuntu Software Center", search for "ia32-libs", click "install"

Vassilis

TEDx Athens registration is open

10/12/2012

TEDxAthens seeks to develop and leverage the TED experience at a regional level, bringing together innovators and inspirational speakers in Athens, Greece.

It organizes a yearly event with speakers (mostly entrepreneurs) from all around the world. For more info and to apply fo rthe event:
"The subject for this year is "The Ones Who Do", extending invitations to visionary individuals from a variety of fields challenging commonly held preconceptions and pre-established boundaries in their field. The Ones Who Do are individuals pushing boundaries dreaming of a different world; the One Who Do seek to find ways of making their ingenuous vision an everyday reality. Any individual challenging widely-held preconceptions regarding how the world works or how the world should work redefines not only our perception of the world but also how our actions might affect the world. Our choice of subject is not only topical but urgent: we need to be active in the way we approach the world itself."

http://2012.tedxathens.com/
http://blog.tedxathens.com/

How to select a string in Excel and return all values in the cell adjacent to the string

10/12/2012

You will need to open the VBA editor (Alt - F11) and click on "Insert", "Module". Paste this code into the module.
VB: Public Function FindSeries(TRange As Range, MatchWith As String) For Each cell In TRange If cell.Value = MatchWith Then x = x & cell.Offset(0, 1).Value & ", " End If Next cell FindSeries = Left(x, (Len(x) - 2)) End Function

The use this function to find your string in the excel book and return all adjacent value

=findseries(A1:B7,"abc") where

A1:A7 contains the range where the function should search
Column A contains the text string you want to look for
Column B contains the values you want to return

This fix was picket up here.

Zoe

Massively renaming files in linux using one command

10/10/2012

Use the command: rename -v 's/sdf/mol/' *.sdf if you want to massively rename *.sdf files to *.mol or for any other renaming under linux.

Zoe