[gmx-users] SO4 ion

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 19 21:37:54 CET 2011

simon sham wrote:
> Hi,
> I have a crystal structure with several SO4 ions.
> According to the online manual, the source is ffgmx.rtp. But I could not 
> find it in
> /gromacs/share/top directory. I also could not find it in several force 
> field files.

You haven't said which Gromacs version you're using, but if it's in the 4.5.x 
series, there has been a complete overhaul of force field organization.  So 
there are no more "ff*.rtp" files; they're all in *.ff subdirectories and called 
"aminoacids.rtp" (with a few force fields having lipids.rtp, rna.rtp, and 
dna.rtp).  For instance:

$ grep -R SO4 */*.rtp
gmx.ff/aminoacids.rtp:[ SO4 ]
gromos43a1.ff/aminoacids.rtp:[ SO42- ]
gromos43a2.ff/aminoacids.rtp:[ SO42- ]
gromos45a3.ff/aminoacids.rtp:[ SO42- ]
gromos53a5.ff/aminoacids.rtp:[ SO42- ]
gromos53a6.ff/aminoacids.rtp:[ SO42- ]

> Just curious how people have treated this ion in their simulations.

You're better off not using ffgmx.  The manual describes the reasons for this 
very clearly.  A newer Gromos96 variant might be more suitable, or other 
(potentially better) parameters that might exist in the literature.


> Thanks for your help.
> Simon Sham


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


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