Hi,
Did you check the residue and atom names of water
in the generated topology file?
If the residue name is TIP3 and the water oxygen
name is OH2, they must be replaced by WAT and
O, respectively.
>From my experience so far, a bit old version of
parmed generates "TIP3" and "OH2", while a
newer version generates "WAT" and "O".
Song-Ho Chong
2017-05-08 15:46 GMT+09:00 Sadegh Faramarzi Ganjabad <
safaramarziganjabad.mix.wvu.edu>:
> Daniel,
>
> Thanks for replying to my post. I am using AMBER 16 (pmemd.coda). My system
> is a membrane protein in a detergent , n-dodecyl beta-D-maltoside (DDM)
> micelle. I used CHARMM 36 ff topologies (protein, lipid, detergents .str,
> and water-ions).
>
> toppar_c36_feb16.tgz in
> http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
>
>
> Here is my input argument in parmed
>
> chamber -top top_all36_lipid.rtf -param par_all36_lipid.prm -param
> par_all36m_prot.prm -param par_all36_cgenff.prm -param par_all36_na.prm
> -param ddm2.prm -param par_all36_carb.prm -param par_all36_prot_mod.prm
> -str toppar_all36_lipid_detergent.str -str retinal-pro.str -toppar
> toppar_water_ions_fixed.str -psf pr-ddm-ion-rst3.psf -crd
> pr-ddm-ion-rst3.pdb -box 141.5,142.5,134.7
>
> outparm test.prmtop test.inpcrd
>
> Please let me know if you need to know any other details.
>
> Thanks,
> Sadegh
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>
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Received on Mon May 08 2017 - 08:30:04 PDT
