On 1/15/15 12:57 PM, Jennifer Vo wrote:
Dear Justin,
Many thanks for your answer. I tried
grep " SI " *.*
That won't return anything if what you posted before was accurate. The atomtype
in question was "P,SI" unless you modified the error message. grepping for " SI
" (e.g. with a space on either side of it) won't match "P,SI" in anything.
-Justin
in the whole working directory but nothing found. Where could it be if I
have to search?
Thanks a lot again.
Regards,
Jennifer
On Thu, Jan 15, 2015 at 6:44 PM, Justin Lemkul <[email protected]> wrote:
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
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
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University of Maryland, Baltimore
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==================================================
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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