From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Sun Sep 13 2020 - 09:01:52 CDT
Dear all,
I created .psf and .pdb files for a (8.0) CNT successfully. CNT was then
solvated with no error. As soon as I run the equilibration step for the
solvated CNT (CNT simulation), using CHARMM36 (C36) I recieve the following
error:
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C C (ATOMS 1 9)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C C (ATOMS 1 9)
I put the following parameter files in my configuration files (.conf file
is attached):
paraTypeCharmm on
parameters ../toppar_c36_jul20/par_all36m_prot.prm
mergeCrossterms yes
parameters ../toppar_c36_jul20/par_all36_lipid.prm
parameters ../toppar_c36_jul20/par_all36_carb.prm
parameters ../toppar_c36_jul20/par_all36_na.prm
parameters ../toppar_c36_jul20/par_all36_cgenff.prm
parameters ../toppar_c36_jul20/toppar_water_ions-cmt.str
The equilibrium simulation is perfectly working for a solvated amino acid
(AA simulation), but as soon as it comes to CNT I receive the mentioned
error.. Besides, the CNT simulation works well when I switch to C27
(par_all27_prot_lipid.prm). It seems the problem is the force field. I
don't know what is wrong. Would be thankful to guide me.
All the Best,
Zeynab
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