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

[Justin Lemkul]

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 <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.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================