[gmx-users] Atomtype P,SI not found from grompp

Justin Lemkul jalemkul at vt.edu
Thu Jan 15 22:43:16 CET 2015

On 1/15/15 1:58 PM, Jennifer Vo wrote:
> Dear Justin,
> Thanks again! I have downloaded the topology from Automated Topology
> Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the
> existing molecules.
> Checking all of the *.itp file with both  GROMOS 54A7  and GROMOS 534A6
> force field for all of the NADPH they provided, I see all of these have the
> "P,SI" type.
> I would like to ask for your advice in this case.

Sounds like an error to me.  Distributing topologies that trigger fatal errors 
is probably not what they intended, so I suggest you make them aware of this 
problem.  P and SI have the same nonbonded parameters, so you're safe to simply 
replace the "P,SI" with the proper atom type in this case.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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