[gmx-users] Atomtype P,SI not found from grompp
jalemkul at vt.edu
Fri Jan 23 17:54:45 CET 2015
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
> 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.
> 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
>>> 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 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
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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
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