Re: using NAMD with CHARMM36 ff

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sun Jan 18 2015 - 11:46:38 CST

Maria,

Try to add 'par_all36_carb.prm' among parameters. I suppose that you
have no carbohydrates, but also you have no atoms from cgenff, and ff
developers advised to add all prm files . 'toppar_water_ions_namd.str'
usually performs well with NAMD. If problem persist, try to generate psf
with CHARMM gui (http://www.charmm-gui.org/)

Branko

On 1/18/2015 2:26 AM, Maria Bykhovskaia wrote:
> Hi,
> I tried to use ChARMM36 force field, and I am getting the message:
>
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2
>
> my system does not have the atom type OC2D2
>
> It runs with Charmm27 without errors. The system includes a protein
> and membrane with water (TIP3) and ions (POT, CLA, CAL), psf was
> generated with VMD, and Charmm36 topology was used to build the lipid
> bilayer.
>
> My input file looks this way:
>
> paraTypeCharmm on
>
> parameters par_all36_lipid.prm
>
> parameters par_all36_prot.prm
>
> parameters par_all36_cgenff.prm
>
> parameters toppar_water_ions_namd.str
>
> mergeCrossterms yes
>
> Will appreciate any suggestions.
>
> Thanks,
>
> Maria
>
>
>
>

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