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

[Justin Lemkul]

On 1/23/15 11:51 AM, Jennifer Vo wrote:
> 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?
>

No.  The comment does not tell you that "P,SI" is an atom type.  It tells you 
that the angle parameter there is applicable to either P or SI in the first 
position (atom i), OA in the second position (atom j), then either CHn or P in 
the last position (atom k).  The available atom types for the force field are in 
atomtypes.atp.  If it's not there, it's not real.  I recall our previous 
discussions about the source of the topology.  Hopefully you have alerted the 
ATB developers to the erroneous topology that they're distributing.

If your atom is a phosphorus, the atom type is P.  Don't change it.  If the 
parameters are sub-par, then derive new ones or choose a better force field.

-Justin

> 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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-- 
==================================================

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

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