PCGAMESS/Firefly

I am somewhat of a hobby molecular modeller and have had much sucess with PCGAMESS a piece of software orginally based on GAMESS US and since 1999 an independant project developed by Moscow State University in the group of Prof Granovsky.

Until recently this software only ran on LINUX and Windows however much to my delight I recently recieved an e-mail from Prof Granovsky giving me details of the beta test for program for Firefly running on Mac OS X. I eagerly downloaded onto a quad core mac pro and registered the binaries along with Bret Bodes MacMolPlot.

The Mac version is very intuatively laid out and once the input file is generated in MacMolPlot the user simply draggs the input file to the icon corresponding to the number of required cores. I have carried out a few simple calculations and found it to be both stable and reliable.

I found a great tutorial posted here on pc gamess.

Chem Draw Woes

So I am one of these mac fanboys I love my mac however one piece of software has given me no end of problems. ChemDraw you either love it or hate it. It is an incredibly powerful piece of software with some pretty bad luck with OS X 10.5. In this post I am going to be looking at one pretty good alternative to ChemDraw.

ChemAxon MarvinSketch - Free for academic use

MarvinSketch is part of the larger ChemAxon suite of applications, written in Java it will work equally well on OS X, Windows and Linux. Its friendly intuitive interface is great for migrating from ChemDraw, you can even set out the menubars with a chemdraw look and feel although I find the Marvin layout much more intuitive. MarvinSketch has built in templates for many structures and more importantly journal specifications.

The acid test for me was how quickly can I draw a porphyrin and does it look right. The answer was in less than 30 seconds and a quick 2d clean made it look pretty good. I love the UI for rotation just select the molecule and hover over the selection and drag (see screen shot green molecule). There a built in templates for constructing polymers and a variety of R groups. The fully licensed version includes a whole treasure chest of plug-ins for everything from property estimation to naming and conformer search. All in all I would highly recommend MarvinSketch to anyone who wants to try something different

http://chemaxon.com/

For lists of chemistry software visit the macs in chemistry blog.

Update:

One small annoyance arrises from the ease at which ChemDraw allows users to insert abbreviated structures such as OC12H25, MarvinSketch however requires a much longer winded process involving drawing the structure and setting a contraction label.

Who am I

As the blog suggests my name is Chris Wilson. I was born in Wolverhampton and spent both my undergrad and post grad in Hull. I am now working as a research scholar (post doc) at The University of Pennsylvania. I  was trained as an organic chemist and cut my teeth on both porphyrin and dendrimer chemistry my interests now lie in the soft self-assembly and self-organization of condensed matter. You can find more about me at my home page

Dr Chris Wilson

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