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

[Kia.Balali-Mood@ed.ac.uk]

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!
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html

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!

Kia 

> 
> 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
Summerhall
Edinburgh, EH9 1QH
Tel. +44 (0)131 650 6142
Fax. +44 (0)131 650 6576
leaflet.vet.ed.ac.uk