[gmx-users] Fatal Error: Unknown bond_atomtype OS. Simulating membrane protein in DPC micelle. PLEASE HELP!!!

[Justin Lemkul]

On 7/18/16 11:33 PM, Tapash, Arifuzzaman wrote:
> Hi all,
>
> I'm a new user of Gromacs. I have completed the first two tutorials  ('Lysozyme in Water' and the 'KALP-15 in DPPC')by Justin Lamkul recently.
>
> Now, I'm trying to simulate a membrane protein (1RKL) in a micelle of DPC. I have collected the DPC micelle (m65.pdb - 65 DPC molecules)  from Dr. Tieleman's lab website. I also collected the 'dpc.itp' file from the same website. I'm trying to do this simulation following the 'KALP-15 in DPPC' tutorial.
>
> I have oriented the protein in correct direction and done 'pdb2gmx' on the protein molecule. Then, I modified the gromos force field (ffbonded and ffnonbonded) and the topology (topol.top) file following the tutorial.
>
> I have prepared the DPC topology file (topol_dpc.top) by modifying the 'topol_dppc.top' file provided at that tutorial.
>
> I hope I haven't done any mistake upto that point.
>
> Now, I'm stuck in Step-3 (1. Orient the protein and membrane).
> When I was using the grompp command (gmx grompp -f minim.mdp -c m65.gro -p topol_dpc.top -o em.tpr), I am getting an error message saying-
>
> "Unknown bond_atomtype OS"
>
> Then I checked the 'dpc.itp' file, and found that in some places of that file 'OS' atomtype is mentioned, but in the "atomtypes.atp" file in the gromos forcefield, I didn't find any atomtype "OS" defined.
>
> I'm stuck in this stage. How to solve this? Do I have to modify the dpc.itp file or the atomtype.atp file?
>

The .atp file is only read by pdb2gmx.  If there are additional parameters that 
are required, you need to incorporate them via #include mechanism with an .itp 
file that defines them or by modifying ffnonbonded.itp (which is the primary 
point of the KALP-15/DPPC tutorial).

-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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