From: NEHİR NALINCI (nehirnalinci_at_iyte.edu.tr)
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.
From: "Brian Radak" <brian.radak_at_gmail.com>
To: "namd-l" <namd-l_at_ks.uiuc.edu>, "NEHİR NALINCI" <nehirnalinci_at_iyte.edu.tr>
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:
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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