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
included.
vmd > networkSetup network.config
Info) Using plugin psf for structure file
../1.network_preparation/1pii_2ligs.psf
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
../1.network_preparation/2ligs_amd4a_3.dcd
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.
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Received on Thu Aug 20 2020 - 13:30:02 PDT
