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

Dilip H N cy16f01.dilip at nitk.edu.in
Sun Oct 8 19:04:26 CEST 2017

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..??

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...

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...??)

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

Any suggestions are appreciated...

With Best Regards,

Ph.D Student

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