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CHARMM TIP3P model or classic TIP3 model?
袁曙光 2013-7-8 15:59
Each time when we run pdb2gmx in gromacs, if we select charmm36 FF for our system, we always have following informations: Select the Water Model: 1: TIP3P TIP 3-point 2: TIP4P TIP 4-point 3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS), re ...
7113 次阅读|没有评论
could it flip?
袁曙光 2013-5-26 19:12
The GPCRDOCK 2013 contest hosted by Scripps Institute was finished months ago with the released of 5HT1B and 5HT2B crystal structures bound with agonist molecule Ergotamine. I also attended this event and compared my models with the crystal structure. My models were built in Modeller templ ...
个人分类: 科研笔记|3019 次阅读|没有评论
Membrane permeability
袁曙光 2013-5-23 23:12
In the late 1800's, E. Overton discovered that substances that dissolve in lipids pass more easily into the cell than those that dissolve in water. This was some of the first evidence that cells were surrounded by a lipid membrane. The phospholipid membrane of cells can greatly modify the p ...
个人分类: 科研笔记|4537 次阅读|没有评论
Class F G-protein-coupled receptor released
袁曙光 2013-5-2 16:34
Structure of the human smoothened receptor bound to an antitumour agent Chong Wang,Huixian Wu,Vsevolod Katritch,Gye Won Han,Xi-Ping Huang,Wei Liu,Fai Yiu Siu,Bryan L. Roth,Vadim Cherezov Raymond C. Stevens Nature(2013) doi:10.1038/nature12167 Received15 January 2013 Accept ...
个人分类: 科研笔记|2592 次阅读|没有评论
Desmond 3.4.0.2 source code released
袁曙光 2013-4-10 02:29
This new version finally update VIPARR tool from 3.x into 4.x which can handle NBFIX terms in CHARMM 36 protein FF and latest CHARMM 36 LIPIDS FF parameter sets. ____ &nbs ...
个人分类: 科研笔记|2874 次阅读|没有评论
A Simulation Work Published on CELL
热度 1 袁曙光 2013-3-4 23:43
In most people's minds, modeling and simulation work can only be released in journal with IF 3-5 such as: J Chem Inf Model or PLOS Computational Biology and so on. However, if the work is good enough, it is still possible to be accepted by nowadays so called "CNS (CELL, Nature and Science)". He ...
个人分类: 科研笔记|3398 次阅读|2 个评论 热度 1
SQLite Manager, a manager of Desmond .dms file
袁曙光 2013-2-23 22:35
The Desmond .dms file, which can be converted from Schrodinger Maestro file format .cms with command mae2dms, is quite difficult to modify by text editor. However, the .dms file actually is a SQLite database file, and w ith Sqlite3 command or SQLite Manager we can easily handle .dms file. Thanks ...
个人分类: 科研笔记|3718 次阅读|没有评论
SUSE Linux Enterprise 11 SP3 Authorized Beta Program
袁曙光 2013-2-15 00:37
SUSE Linux Enterprise 11 SP3  Authorized Beta Program
Words from SUSE developer: "We plan to have a call together with each Beta release, where we highlight some topics. Let me invite you to the Kick Off call in our Beta Test, where SUSE Linux product managers will present new features in SLE 11 SP3..."
个人分类: Linux相关|4558 次阅读|没有评论
Compiling Desmond 3.4 from source code.
袁曙光 2013-2-14 17:30
Compiling Desmond from source code seems to be the most challenging work that I've ever found especially the latest V3.4. Fortunately, it was successfully compiled these days. During the sampling test, 2 CPU can even get up to 4 ns /day with NVE ensemble for a typical membrane system which is real ...
个人分类: 科研笔记|3531 次阅读|没有评论

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