From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 15 2020 - 10:29:14 CDT
Hello
As you can see from the log file below, namd 2.13, on minimization,
complains about the lack of vdW for atom type OC2D1. Actually such atom
type, if it exists at all, is not present in either the .str file for my
ligand or the general .psf file for my receptor made of nuclei/prot, on
attempt to minimization, generated with CHARMM36 FF jul19, i.e the latest,
which includes CGenFF 4.3.
As I plan to carry out QMMM, I added the to the .str vdW the line
OC2D1 0.00 0.000 0.000
getting the same request of vdW for atom type OC2D1
>
> Warning: DUPLICATE vdW ENTRY FOR IGR1
> PREVIOUS VALUES sigma=3.99123 epsilon=0.52 sigma14=3.99123 epsilon14=0.52
> USING VALUES sigma=3.52796 epsilon=0.23 sigma14=3.52796 epsilon14=0.23
> Warning: DUPLICATE vdW ENTRY FOR CG3RC1
> PREVIOUS VALUES sigma=3.56359 epsilon=0.032 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.56359 epsilon=0.032 sigma14=3.56359
> epsilon14=0.032
> Warning: DUPLICATE vdW ENTRY FOR NG2S1
> PREVIOUS VALUES sigma=3.29633 epsilon=0.2 sigma14=2.76179 epsilon14=0.2
> USING VALUES sigma=3.29633 epsilon=0.2 sigma14=3.29633 epsilon14=0.2
> Warning: DUPLICATE vdW ENTRY FOR CG3C52
> PREVIOUS VALUES sigma=3.59923 epsilon=0.06 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.59923 epsilon=0.06 sigma14=3.59923 epsilon14=0.06
> Warning: DUPLICATE vdW ENTRY FOR OG2D1
> PREVIOUS VALUES sigma=3.02906 epsilon=0.12 sigma14=2.49452 epsilon14=0.12
> USING VALUES sigma=3.02906 epsilon=0.12 sigma14=3.02906 epsilon14=0.12
> Warning: DUPLICATE vdW ENTRY FOR CG331
> PREVIOUS VALUES sigma=3.65268 epsilon=0.078 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.65268 epsilon=0.078 sigma14=3.65268
> epsilon14=0.078
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D1
>
thanks for advice
francesco pietra
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