VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Aug 09 2011 - 17:42:32 CDT

If you calculate the ions needed to neutralize and reach a given concentration yourself, you can use autoionize to add them with the -nions flag. (Note that concentration = #ions * 55.5/ # water molecules ). NAMD will sum the charge correctly and confirm your system is neutral.

At the risk of sounding demanding, this is something that has been raised many times by myself and others for months and REALLY needs to be fixed if VMD is going to be usable for modern forcefields.

On Aug 9, 2011, at 4:01 PM, Anna Whitney wrote:

> Hi,
>
> I'm trying to add ions to a system consisting of a protein with a ligand parameterized using CGenFF, a DOPC/DOPE membrane, and water. VMD's Autoionize plugin returns a non-integral charge, however. When I check the charge on the ligand using
> set sel [atomselect top "resname TAK"]
> measure sumweights $sel weight charge
> I also get a non-integer (and a much higher charge than I should), while all other components of the system have integral charges according to VMD. I don't think Autoionize is giving me anything useful, based on how wrong it is about the initial charges.
>
> Previous messages on the mailing list seem to indicate that this problem can be caused by VMD misreading PSF files with atom types longer than four characters, which my PSF does have, from CGenFF. However, I couldn't find a workaround on the mailing list or anywhere else- is there any way to get VMD to correctly read charges from a PSF that includes longer-than-four-character atom types? Alternately, is there some other way of adding ions (to neutralize and/or bring to a certain concentration) that doesn't involve VMD's interpretation of the charge from the PSF?
>
> Thanks,
> Anna Whitney