From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Aug 04 2021 - 22:32:11 CDT
it is simple as stated that the information for the bond between the two atoms is missing in your parameter file. Please check this in your parameter file, and to solve this or to get the bond length you may check search the CHARMM repository or look for literature.
If you still can't find this information, then you have to go to the CHARMM-GUI and upload the molecule to get the parameters. You may also try to check with CGENFF server, by uploading mol2 format of your molecules. If none of this work, then you need to procced for the structure optimization using FFTK toolkit available in VMD.
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of samaneh ghanbari <ghanbari.samaneh_at_gmail.com>
Sent: Tuesday, August 3, 2021 22:05
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: namd-l: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS
Thanks for the help Mr Shekaari. Your suggestion solved the issue. But alternatively I had this problem for other atom types that I wrote like ATOM TYPE NHL in the parameter file. However, now I am getting a new error stating, " FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL3 CTL2 (ATOMS 490 488)"
I am unable to understand the reason behind it. Could you help me, please?
-- Sincerly Yours Miss.Ghanbari
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST