[gmx-users] Atomtype P,SI not found from grompp
quyviolet at gmail.com
Fri Jan 23 15:52:29 CET 2015
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.
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
>> "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 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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