Re: missing parameters.

Date: Thu Nov 16 2017 - 01:28:42 CST

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.

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