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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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