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

[Justin Lemkul]

On 1/15/15 12:20 PM, Jennifer Vo wrote:
> Dear Experts,
> I ran a grompp (gromos53a6 ff)
> grompp -f em.mdp -c complex2_solvated.gro -p topol.top -o complex.tpr
>
> and it generated the error
> Atomtype P,SI not found
>
> I checked the gromos53a6.ff/atomtypes.atp and see there are P, SI in the
> list
>     SI  28.08    ;     Silicon
>     P  30.97380 ;     Phosphor
>
> And there is no P, SI in my complex2_solvated.gro file! I really do
> appreciate for any help.

It's an atom type, so it won't be in a coordinate file.  Something in a topology 
or force field file is specifying something called "P,SI" as an atomtype. 
That's clearly not sensible.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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