Re: autoionize script

From: Olya Kravchenko (okrav_at_ucdavis.edu)
Date: Mon May 17 2004 - 14:00:12 CDT

Hi Anna! Look at your topology file and see whether sodium atom is described
in the section in the begining of topology file:

MASS 191 SOD 22.989770 NA ! Sodium Ion

 and whether it has the same name (not NA, but SOD), and also look through
your topology file and whether you have residue entry for sodium ion, like
this:

RESI SOD 1.00 ! Sodium Ion
GROUP
ATOM SOD SOD 1.00
PATCHING FIRST NONE LAST NONE

Also compare your pdb file and your topology file and make sure you have the
same name for sodium ion in both topology and pdb file. A message like this
usually comes up if something is not described in topology file you are
using. Hope that helps.

Olga

On Sunday 16 May 2004 11:21 am, amodzelewska_at_dns.iimcb.gov.pl wrote:
> Hi,
> I wanted to ionize my model with the autoionize plugin v.1.1 in VMD
> v.1.8.2. I didn't succeed because of the error message that ions.top file
> was missing. I prepared this file by cutting some lines from the
> top_all27_prot_lipid.inp file (in attachement). I suppose the script was
> working correctly, the structure was read, 20 sodium ions were added, but
> when the "ionized" files were being constructed the process was
> interrupted with error messages: "unknown residue SOD". Does anybody have
> an idea why?
> Thanks
> Anna
>
>
>
>
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