From: Chitrak Gupta (
Date: Wed Sep 09 2015 - 08:17:50 CDT

Hi Christopher,

Thanks a lot for your continued help.

I just realized that when I was creating the original PSF file for my
residue, I did not change the charges of the aliphatic hydrogens to 0.0900
(every atom was set to 0). I completed the charge optimization (and removed
the aliphatic hydrogens as recommended), and that is when I realized that
those atoms still have a 0.0000 charge.

Do I have to re-do the entire protocol with the correct aliphatic H
charges? Or can I simply manually change it in the PSF and proceed normally
from this point?


On Tue, Sep 8, 2015 at 4:10 PM, Mayne, Christopher G <>

> The guessing algorithm gives you a decent place to start from; hopefully
> you would need to remove fewer entries than you would have had to add, and
> thus, saving you time.
> The water molecules aren't actually bonded to your molecule. When loading
> in files that don't contain explicit bonding information, e.g., PDB, VMD
> employs heuristics to guess where the bonds are based on atom-to-atom
> distances; once the bonds are defined, they apply to all frames. Since the
> water is close to your molecule in the first frame of the optimization, VMD
> thinks there's a bond and applies is to all subsequent frames.
> Regards,
> Christopher Mayne
> On Sep 8, 2015, at 2:57 PM, Chitrak Gupta wrote:
> Hi Christopher,
> Thanks for directing me to this link.
> So from what I understand, for anything but really small molecules, it is
> a good idea to use your chemical intuition to select donor and acceptor
> atoms, is that correct?
> I re-did this step, this time manually selecting the donors and acceptors--047d7bdc102e3f8d0a051f504f3f--