Re: Equilibration of a solvated CNT using C36

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 13 2020 - 13:14:18 CDT

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are you sure that the atom type "C" is the correct atom type for CNT atoms?

just look into the parameter file:

MASS 20 C 12.01100 C ! carbonyl C, peptide backbone
MASS 21 CA 12.01100 C ! aromatic C
MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH
MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons
MASS 26 CPH2 12.01100 C ! his CE1 carbon
[...]

axel.

On Sun, Sep 13, 2020 at 10:06 AM zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:

> 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
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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