using amber force field in namd simulation

From: İmren Bayıl (ib57001_at_student.gaziantep.edu.tr)
Date: Wed Jun 29 2022 - 05:32:57 CDT

• Next message: Mükerrem Tüfekçioğlu: "Force and RMSD Values for TMD"
• Previous message: Ebru Çetin: "Snakemake with NAMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

I want to apply md simulation my complex structure which is
dna-ligand.using tleap I wrote inpcrd and prmtop files for my complex
structure.occurred the structures are complex_clean2_wat.prmtop and
complex_clean2_wat.inpcrd.
The problem is that namd simulation.I am not sure that my
namd configuration file is true for md simulation.I shared my files also
attached .
Could anybody help me this files is true for complex structures ?

• application/octet-stream attachment: 01-all_min.namd

• application/octet-stream attachment: 02-water_equ.namd

• application/octet-stream attachment: 03-equ_200.namd

• application/octet-stream attachment: 04-equ_250.namd

• application/octet-stream attachment: 05-equ_300.namd

• application/octet-stream attachment: 06-01.namd

• Next message: Mükerrem Tüfekçioğlu: "Force and RMSD Values for TMD"
• Previous message: Ebru Çetin: "Snakemake with NAMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST