[gmx-users] Regarding charges for atoms in a molecule

Justin Lemkul jalemkul at vt.edu
Sun Oct 8 19:10:04 CEST 2017

On 10/8/17 1:04 PM, Dilip H N wrote:
> Hello,
> I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
> ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
> abc.gro command.
> 1] In the topology file, the charges for each atom are assigned. from where
> are these charges assigned..?? is it from the .rtp file, itp file..??

Charges are in the .rtp file (see the manual for how pdb2gmx works).

> 2] If so, I compared the charges in the generated topology file and in the
> merged.rtp file, but the charges are different in both the files...

If you have just a single glycine, and you applied N- and C-terminal 
patches to it, the residue is modified according to the .n.tdb and 
.c.tdb entries. This is probably where the differences lie.

> 3] I even checked in the ffnonbonded.itp file, but here for all the atom
> types the charges are 0.00 only...(why is this so...??)

Because those charges are never used for anything and have no meaning.

> So, from where (or) where are the charges specified..in which file

The "real" answer is that they are derived by those of us who work very 
hard to parametrize force fields, and you can get information on how 
that was done by reading the appropriate literature. This is really 
important to do so you understand how the force field works, pros and 
cons, etc. The implementation of charges into various files is just a 
technical detail.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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