From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Nov 16 2017 - 06:19:04 CST
The two files you mention are from two different versions of the CHARMM
force field. You should not mix and match, because some parameters have
changed and their occurrence in different files has been reorganized.
You can always get an up-to-date version of the entire ff database from
On Thu, Nov 16, 2017 at 2:28 AM, NEHİR NALINCI <nehirnalinci_at_iyte.edu.tr>
> I use CHARMM files from vmd plugins "par_all36_na.prm and
> par_all27_prot_lipid_na.inp". I tried to do like tutorial files. When I
> run the simulation, I get errors that 12 dihedral parameters are missed.
> Thank you.
> *From: *"Brian Radak" <brian.radak_at_gmail.com>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>, "NEHİR NALINCI" <
> *Sent: *Wednesday, November 15, 2017 5:10:46 PM
> *Subject: *Re: namd-l: missing parameters.
> This is likely a topology and parameter problem. What force field are you
> using? What format? XPLOR? AMBER? How did you construct the system?
> On 11/15/2017 07:53 AM, NEHİR NALINCI wrote:
> Hİ everyone,
> I took single strand DNA which contains A, G, C, T from the protein data
> bank, but I didn't run the my simulation, because some dihedral parameters
> are missing in the parameter files such as " ON1 CN1 CN3T CN3 ". I tried
> to add all paramater files to take care of these dihedrals. How can I solve
> this problem?
> Thank you for interest.
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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