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

[Jennifer Vo]

Dear Justin,
Many thanks for your answer. I tried
grep " SI " *.*
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 <jalemkul at vt.edu> 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
>
> --
> ==================================================
>
> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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