[gmx-users] adding Na and cl ions to pdb structure

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear All
> How can I add one Na ion and cl ion  to a pdb structure?
> for example I want to have a pdb file which contains my protein and one 
> Na and one Cl ion.
> by pymol?How?
> by manipulating pdb file?How?
> 

If you want to place them in a known location, just write their coordinates in 
by hand.  If you want them inserted randomly in the box (in vacuo?), then use 
genbox -ci -nmol for both Na+ and Cl-.

-Justin

> Thanks in advance
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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