From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Aug 03 2021 - 09:16:45 CDT
In your system, there is a bond between atom types CEL3 and CTL2. In the
force field parameter files you provided in the input script for NAMD,
no parameters are defined for that combination of atom types. NAMD thus
doesn't know how to compute forces for that pair of atoms, and bails. A
quick grep through CHARMM parameter files suggests that you are missing
toppar_all36_lipid_sphingo.str, which is where the parameters for
sphingolipids are defined.
-Josh
On 8/3/21 10:05 AM, samaneh ghanbari wrote:
>
> Dear all
> 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
-- Josh Vermaas vermaasj_at_msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!omJmNVPlO-Fx3T-honMdksP_g2XcIvMtGye1XVrcwyg402hiWuDIRY4bRWiY3_dxmg$
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