From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Nov 19 2019 - 13:12:04 CST
HI Mikhail,
You'd also likely need to load in the standard lipid parameters (par_all36_lipid.prm), as what is in the toppar directory is an extension of the standard CHARMM parameter set. Giacomo's approach will get you the missing terms specific to SDS that aren't found in typical lipids.
-Josh
On 2019-11-19 10:57:36-07:00 Giacomo Fiorin wrote:
Hello Mikhail, the stream file suggested by Josh includes both the topology template ("top" part) and the parameters ("par" part) of the CHARMM force field for detergents.
You can extract what is enclosed between the two fields below:
read para card append flex
..
end
And NAMD can read that as a "parameters" file.
You may need to do the same for sodium as well, starting from "toppar_water_ions.str".
Giacomo
On Tue, Nov 19, 2019 at 12:04 PM Mikhail Suyetin <msuyetin_at_gmail.com<mailto:msuyetin_at_gmail.com>> wrote:
Dear Josh,
Sorry for the late answer.
Great! Many thanks for this.
Another question, can you give me a hint where can I find a param file (file with constants for bonds, angles, vdw interactions) for the simulation of sodium dodecyl sulfate in NAMD?
Kind Regards,
Mikhail
On Thu, 14 Nov 2019 at 17:46, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Hi Mikhail,
SDS is in toppar_all36_lipid_detergent.str in the CHARMM 36 force field. The sodium would come from a solvate command to neutralize the system.
-Josh
On 2019-11-14 09:09:43-07:00 owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> wrote:
Dear All,
Hope you are doing great.
I would like to ask you, does anybody have files (psf, pdb, topology) for performing simulations for sodium dodecyl sulfate:
https://en.wikipedia.org/wiki/Sodium_dodecyl_sulfate
Kind Regards,
Mikhail
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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