[gmx-users] top file

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 8 13:28:45 CEST 2012

On 7/8/12 3:12 AM, Shima Arasteh wrote:
>   Dear gmx users,
> I have gotten 2 topology files from a unique simulation ( a protein in water) with gmx and CHARMM36. I  know the charges of atoms derived by PRODRG and CGENFF are different, but I'm wondering if the total charge which is visible in top file, is supposed to be the same? What items are expected to be the same? or be in agreement?

The total charge is given in the qtot column of the .top file.  In theory, at a 
given protonation state, any protein should have the same net charge under any 
force field.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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