From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Tue Jan 08 2019 - 13:58:19 CST
You need to write a parameter file for graphene containing bond lengths, angles and the related lennard jones parameter. See bionanotechnology tutorial.
-- Regards, Ashkan Shekaari, Ph.D Candidate in Solid State Physics, K. N. Toosi University of Technology, Tehran, Iran ----- Original Message ----- From: Nasim Rajabi <nr8869_at_REMOVE_yahoo.com> To: NAMD List <namd-l_at_ks.uiuc.edu>, namd_at_ks.uiuc.edu Sent: Tue, 08 Jan 2019 01:45:43 +0330 (IRST) Subject: namd-l: CHARMM force field for Hydrogen bond? hi everyone i have a functionalized graphene nanopore which the unsaturated carbon atoms at the pore edge were bonded with the H atoms,i solvate and ionize the system using vmd but when i want to minimize my system using NAMD with CHARMM27 force field i got this error: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 518 925) but i cant find bond parameters for hydrogen with carbon in any CHARMM force fields!!! Can someone help me to solve this problem???
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