Hi,
As stated in the manual (the table in 32.9 that lists supported
topology formats) there is only limited support for PSF writes; the
only fully-supported topology for writes is Amber topology files. More
recent versions of cpptraj (to be safe use the github version, but the
AmberTools 20 version does it as well I think) will write some
additional PSF terms (angles, dihedrals, impropers); however, things
like CMAP terms are definitely not yet supported. Cpptraj was never
intended to be used as a parameter/topology conversion tool (even
though some of that has crept in over the years). Parmed might have
better support for something like this.
-Dan
On Thu, Aug 20, 2020 at 4:23 PM Lod King <lodking407.gmail.com> wrote:
>
> 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 Fri Aug 21 2020 - 14:00:03 PDT
