Re: missing parameters.

Date: Mon Nov 20 2017 - 05:32:44 CST

Hi again,
I have one question, which parameter file is suitable for thymine?

From: "Giacomo Fiorin" <>
To: "namd-l" <>, "NEHİR 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:
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On Thu, Nov 16, 2017 at 2:28 AM, NEHİR 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" < [ | ] >, "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 
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