David,
Thanks for replying. Here is what I put on parmed
chamber -top top_all36_lipid.rtf -top top_all36_prot.rtf -top
top_all36_carb.rtf -top top_all36_cgenff.rtf -param par_all36_lipid.prm
-param par_all36m_prot.prm -param par_all36_cgenff.prm -param
par_all36_na.prm -param par_all36_carb.prm -param par_all36_prot_mod.prm
-str toppar_all36_lipid_detergent.str -str retinal-depro.str -toppar
toppar_water_ions_fixed.str -psf m2/all-ion.psf -crd all-ion.pdb -box
75.4,75.13,83.8
And I get
Creating chamber topology file from PSF m2/all-ion.psf, RTF files
[top_all36_lipid.rtf, top_all36_prot.rtf, top_all36_carb.rtf,
top_all36_cgenff.rtf], PAR files [par_all36_lipid.prm, par_all36m_prot.prm,
par_all36_cgenff.prm, par_all36_na.prm, par_all36_carb.prm,
par_all36_prot_mod.prm], and STR files [toppar_all36_lipid_detergent.str,
retinal-depro.str, toppar_water_ions_fixed.str]. Coords from all-ion.pdb.
Using CMAP. Box info [75.4, 75.13, 83.8, 90.0, 90.0, 90.0]. GB Radius set
mbondi.
Action chamber failed
CharmmError: Could not convert dihedral phase to <type 'float'>
I tried to attach the files but it says it is too big to be sent to you.
Thanks,
Sadegh Faramarzi,
Research Assistant
West Virginia University, Department of Chemistry
Email:safaramarziganjabad.mix.wvu.edu
On Mon, Apr 9, 2018 at 6:18 PM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad.mix.wvu.edu> wrote:
> David,
>
> Thanks for replying. Here is what I put on parmed
>
> chamber -top top_all36_lipid.rtf -top top_all36_prot.rtf -top
> top_all36_carb.rtf -top top_all36_cgenff.rtf -param par_all36_lipid.prm
> -param par_all36m_prot.prm -param par_all36_cgenff.prm -param
> par_all36_na.prm -param par_all36_carb.prm -param par_all36_prot_mod.prm
> -str toppar_all36_lipid_detergent.str -str retinal-depro.str -toppar
> toppar_water_ions_fixed.str -psf m2/all-ion.psf -crd all-ion.pdb -box
> 75.4,75.13,83.8
>
> And I get
>
> Creating chamber topology file from PSF m2/all-ion.psf, RTF files
> [top_all36_lipid.rtf, top_all36_prot.rtf, top_all36_carb.rtf,
> top_all36_cgenff.rtf], PAR files [par_all36_lipid.prm, par_all36m_prot.prm,
> par_all36_cgenff.prm, par_all36_na.prm, par_all36_carb.prm,
> par_all36_prot_mod.prm], and STR files [toppar_all36_lipid_detergent.str,
> retinal-depro.str, toppar_water_ions_fixed.str]. Coords from all-ion.pdb.
> Using CMAP. Box info [75.4, 75.13, 83.8, 90.0, 90.0, 90.0]. GB Radius set
> mbondi.
> Action chamber failed
> CharmmError: Could not convert dihedral phase to <type 'float'>
>
>
> And attached are the files.
>
> Thanks,
> Sadegh Faramarzi,
> Research Assistant
> West Virginia University, Department of Chemistry
> Email:safaramarziganjabad.mix.wvu.edu
>
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Received on Tue Apr 10 2018 - 10:00:02 PDT
