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

[Justin Lemkul]

On 1/23/15 9:52 AM, Jennifer Vo wrote:
> 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?

If the parameters provided distort the structure, you need to find or derive 
better ones.  You can't sub in nonsensical atom types and hope for it to work :)

-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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