[gmx-users] Re: finding charges and radii (Shuaib Shahid)

Kia.Balali-Mood@ed.ac.uk Kia.Balali-Mood at ed.ac.uk
Wed Feb 25 13:03:00 CET 2004

Hi Shuaib,

I presume u've Checked the text file (pdb) where u may find them if not..then 
this excellent website (courtesy of Dr Van Alten at Dundee) should help in 
generating charges

Note that GROMACs only auto generates topologies for proteins!

As for the diameter, you can use sybyl if u have it if not use editconf (prog. 
in gromacs..check website www.gromacs.org for details)..to put a box around ur 
lipids and simply work out the diameter from the system dimensions it generates!

Hope this helped!


> Hi,
> i am very new to VMD and gromacs so this question will probably sound very =
> basic.
> I have a file of lipids "pop128a.pdb" and i wanted to know how i can find t=
> he charge and diameter of the headgroups in this and other lipid files. c=
> an i do this in VMD or should i be using another program, such as gromacs=
> , to find this?
> thanks
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Kia Balali-Mood
Laboratory of Membrane Biophysics
Division of Pre Clinical Veterinary Sciences
University of Edinburgh
College of Medicine & Veterinary Medicine
The Vet School
Edinburgh, EH9 1QH
Tel. +44 (0)131 650 6142
Fax. +44 (0)131 650 6576

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