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

[Jennifer Vo]

Dear Justin,
I did try replacing the "P,SI" to "P"  but the ligand was distorted during
energy minimization (error happened excactly at the position of P). Then I
tried replacing "P,SI" to "P, SI" (with one space in between)  according to
the existed gromos54a7 force field but got the error when running grompp:
*Too few parameters on line (62) *

which is the line of "3 P, SI" as following:

;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OA    1    NAP     O1X    1   -0.797  15.9994
    2     H    1    NAP      H4    1    0.295   1.0080      ; -0.502
    3 P, SI    1    NAP     P2B    2    2.585  30.9738
    4    OM    1    NAP     O3X    2   -1.083  15.9994
    5    OA    1    NAP     O2X    2   -0.797  15.9994
Keep playing around by replacing "P, SI" with "PSI" on all files but it
also didn't work,
Could you please help me for a solution in this case?
Many thanks in advance.
Regards,
Jennifer

On Thu, Jan 15, 2015 at 10:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/15 1:58 PM, Jennifer Vo wrote:
>
>> Dear Justin,
>> Thanks again! I have downloaded the topology from Automated Topology
>> Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the
>> existing molecules.
>>
>> Checking all of the *.itp file with both  GROMOS 54A7  and GROMOS 534A6
>> force field for all of the NADPH they provided, I see all of these have
>> the
>> "P,SI" type.
>> I would like to ask for your advice in this case.
>>
>
> Sounds like an error to me.  Distributing topologies that trigger fatal
> errors is probably not what they intended, so I suggest you make them aware
> of this problem.  P and SI have the same nonbonded parameters, so you're
> safe to simply replace the "P,SI" with the proper atom type in this case.
>
>
> -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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