VMD-L Mailing List

From: Andrea Holfelder (andreaholfelder_at_gmx.com)
Date: Wed Aug 31 2011 - 10:35:45 CDT

I used the add ion plug in in vmd and was hoping that after addition of ions,I will be able to get both the ionized.pdb and ionized.psf

 But ionized.psf loads up in vmd and through which I could case the ionized.pdb file but I do not know how I can get ionized.psf file from it ?

 Is there anyway to save the ionized.psf file as well which I will be needing for NAMD simulation.

 I do not want to use the psfgen to create the psf out of ionized.pdb because there are many residues in my pdb file also having different segid and I therefore can not use psfgen which would give them all the same segid and which then has the limit of 9999 residues in it.

 advise something please on creating psf as well pdb file easily from add ions plug in of vmd.