[gmx-users] atom types

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Jul 28 02:54:08 CEST 2004


>    I mean what those atom types stand for.In the structure I have seen only
>5-6 atom types but in the file I have seen like 12 atom types.Why is the
>difference and exactly what each of them stands for.I hope you got my

Check the atom type file for the force field, that should have a comment 
tell you what sort of atom it is.  Other than that, load up the coordinate 
file for the molecule and simple look at it with the atom names turned on 
(using what every graphical program that you use, such as VMD) and work it 
out from the structure.

Other than that, you will have to ask the person that defined that atom 
names, which will be explained if it has been published in the article.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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