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

[Jennifer Vo]

Dear Justin,
Thanks a lot. I tried to use all of the NADPH from ATB (
http://compbio.biosci.uq.edu.au/atb/index.py) and they have the same
problem.
Regarding the "P, SI", ist atom type "P, SI" (with one space in between) is
existed in the gromos 54A7 force field
#define ga_26       120.00      530.00
; P, SI  -  OA  -  CHn, P       95

in file gromos54a7.ff/ffbonded.itp. It means it's not a new atom type, did
I interpret correctly?

Regards,
Jennifer

On Fri, Jan 23, 2015 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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