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

[Jennifer Vo]

Dear Justin,
Thanks a lot, now I got it. I thought P and SI is the two separated atoms
so I searched for them two times. Now the
grep "P,SI" *.*
returned
nap_allatom.itp:    3  P,SI    1    NAP    P2B    1    2.247  30.9738
nap_allatom.itp:   21  P,SI    1    NAP     PA    4    2.315  30.9738
nap_allatom.itp:   26  P,SI    1    NAP     PN    5    2.259  30.9738

should I change "P,SI" to P only?
Regards,
Jennifer

On Thu, Jan 15, 2015 at 7:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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