VMD-L Mailing List

From: andrea spitaleri (andrea.spitaleri_at_iit.it)
Date: Thu Jan 22 2015 - 04:30:00 CST

In addition resname 'Na+' (single not double) works too, at least for me
in 1.9.2

and

On 22/01/2015 10:34, Norman Geist wrote:
>
> Young,
>
> you can use the name of the atoms or for ions even the resname. You
> will find the correct names in your pdb file. If the names contain +
> or - signs, you need to escape these characters in your selection,
> example: resname “Na\+”. You are right in assuming VMD uses the 1^st
> letter of atom names to guess their element, how else should it do
> this? The sodium keyword is just a macro made for the psf world naming
> convention. You can define your own macro for your FF similar to:
>
> atomselect macro myions { resname “Na\+ Cl\-” }
>
> Afterwards you can simply use “myions” in your selections.
>
> Norman Geist.
>
> *Von:*owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *JhonY. I.
> *Gesendet:* Donnerstag, 22. Januar 2015 04:48
> *An:* vmd-l_at_ks.uiuc.edu
> *Betreff:* vmd-l: ion visualization in VMD
>
> Hi,
>
> I'd like to visualize sodium and chlorine ions in VMD using pdb file.
> I used atom name of Na or sodium for sodium ion but It isvisualized as
> if it is nitrogen or sulfur atom.
> It appears thatVMDdetects the first letter of atom name only.
> How can I solve this problem?
>
> Thank you very muchforyour helps in advance.
>
> Best
> Young
> 

-- 
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557