Re: [AMBER] Fast 3-point water residue error for coordinates

From: Sadegh Faramarzi Ganjabad <>
Date: Mon, 8 May 2017 02:46:54 -0400


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

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.

AMBER mailing list
Received on Mon May 08 2017 - 00:00:03 PDT
Custom Search