Re: missing parameters.

From: Lennart Nilsson (
Date: Mon Nov 20 2017 - 11:54:32 CST

Use C36. It contains improvements over C27 for both DNA and RNA.


Den 20 nov. 2017 18:09 skrev "Vermaas, Joshua" <>:
Thymine is a nucleic acid, so in principle either of the nucleic acid force fields would work. You just need to have built your psf in a way that doesn't use both the CHARMM 27 and CHARMM 36 to build up the structure. One or the other, not both. Also, be aware that by default you end up with a ribose sugar, not a deoxyribose like you probably want.


On 11/20/2017 04:38 AM, NEH?R NALINCI wrote:
Hi again,
I have one question, which parameter file is suitable for thymine?
From: "Giacomo Fiorin" <><>
To: "namd-l" <><>, "NEH?R NALINCI" <><>
Cc: "Brian Radak" <><>
Sent: Thursday, November 16, 2017 3:19:04 PM
Subject: Re: namd-l: missing parameters.

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 here:>

On Thu, Nov 16, 2017 at 2:28 AM, NEH?R NALINCI <<>> wrote:
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" <<>>
To: "namd-l" <<>>, "NEH?R 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, NEH?R NALINCI wrote:
H? 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>>

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