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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Received on Mon May 08 2017 - 00:00:03 PDT
