[AMBER] converting prmtop to psf with improper and cross-term info stripped off

From: Lod King <lodking407.gmail.com>
Date: Thu, 20 Aug 2020 13:22:41 -0700

Hi Amber,,

I converted my prmtop to psf using the following command:

parm myparm.prmtop
parmwrite out myparm.psf

However, when I loaded in the VMD terminal, and tried dynamical network
analysis with the provided script. It showed my psf file has no improper
and cross-term info.
PS. my prmtop is created by ff14SB without water box added. 2 ligands are

 vmd > networkSetup network.config

Info) Using plugin psf for structure file

psfplugin) WARNING: no impropers defined in PSF file.

psfplugin) no cross-terms defined in PSF file.

Info) Analyzing structure ...

Info) Atoms: 7005

Info) Bonds: 7068

Info) Angles: 12756 Dihedrals: 31343 Impropers: 0 Cross-terms: 0

Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0

Info) Residues: 454

Info) Waters: 0

Info) Segments: 3

Info) Fragments: 3 Protein: 1 Nucleic: 0

dcdplugin) detected standard 32-bit DCD file of native endianness

dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)

Info) Using plugin dcd for coordinates from file

psfplugin) WARNING: PSF file is incomplete, no angles, dihedrals,

psfplugin) impropers, or cross-terms will be written.

Info) Opened coordinate file carma.psf for writing.

Info) Finished with coordinate file carma.psf.

-code 1 -level 0 -errorcode {CHILDSTATUS 31035 1} -errorinfo {CatDCD 4.0

Reading indices from file 'carma.indices'

Error: no indices found in file.
AMBER mailing list
Received on Thu Aug 20 2020 - 13:30:02 PDT
Custom Search