Re: about *.psf

From: Alessandro Pedretti (alessandro.pedretti_at_unimi.it)
Date: Fri May 27 2005 - 05:30:10 CDT

The CHARMM force field is especially designed for proteins and nucleic
acids. For the small molecules it doesn't contain the parameters for all
atom types. For this reason VEGA ZZ includes some CHARMM templates:

CHARMM -> specific for small molecules and generic use. It requires the
MSI/Accelrys parameter file.
CHARMM22_PROT -> for protein only.
CHARMM22_NA -> for nucleic acid only.
CHARMM22_LIPID -> for lipid (e.g. membrane).

For a non-protein molecule, you could use the CHARMM template, but you need
the MSI/Accelrys parameter file because it includes more atom types then the
standard parameter files (e.g. par_all22_prot.inp).
Best regards

Alessandro Pedretti

----- Original Message -----
From: "" <stting_at_mail.nankai.edu.cn>
To: <namd-l_at_ks.uiuc.edu>
Sent: Friday, May 27, 2005 6:59 AM
Subject: namd-l: about *.psf

> Hi!
> I generated lig1.psf file by VEGA ZZ,but lots of atom type is not
correct!I
> modified some of them by hand. In the top_all_prot.inp, I cannot find
appropriate
> atom type for some atom of the ligand,such as the carbonyl C displayed in
the
> accessory. I tyied to set it as CC or C ,but when I run namd2 ,it says "
FATAL
> ERROR:cannot find bond parameters for bond CA-CC/C in parameter files" .
What
> could I do now?
>
>
>

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