Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Apr 24 2018 - 07:34:01 CDT

Hi Tom,

The "segment" command supports the special patch keywords "first" and
"last" but the "patch" command is expected as a post-segment modification
only.

What usage pattern were you expecting here? It seems weird that a residue
definition would only make sense after a patch has been applied.

Cheers,
Brian

On Mon, Apr 23, 2018 at 8:57 PM, Thomas C. Bishop <bishop_at_latech.edu> wrote:

> Dear NAMD/VMD
> (i'm sending to both since vmd and namd users may independently be using
> psfgen... this was also reported in VMD-l about a year ago but does not
> seemed to have changed.
>
> THe post was originally
> "From: Ashar Malik (asharjm_at_gmail.com)
> Date: Wed Apr 05 2017 - 05:15:38 CDT"
>
>
> It seems that psfgen autogenerate does not recognize the "PATCH" option
> for the AUTO keyword
> as evidenced by
> vmd > auto
> arguments: ?angles? ?dihedrals? ?none?
>
> so line 92 in CHARMMS top_all36_prot.rtf file that reads
>
> AUTO ANGLES DIHE PATCH
> throws an error... presumably b/c psfgen does not know the
> "PATCH"option
> but the edited line
> AUTO ANGLES DIHE
> works as it expected
>
> It seems reasonable (and likely easy fix) that the AUTOGENERATE command
> should work on patches too.
>
> Is this a bug or feature?
> output providedbelow
>
> Thanks in advance for any info
>
> TOm
>
> *************************************************** SESSION DUMP
> **************************
>
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> .........
> vmd > package require psfgen
> topology toppar/top_all36_prot.rtf
> 1.6.4
> vmd > psfgen) reading topology file toppar/top_all36_prot.rtf
>
> psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
> psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
> psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
> psfgen) All comments to the CHARMM web site: www.charmm.org
> psfgen) parameter set discussion forum
> psfgen)
> psfgen) Created by CHARMM version 36 1
> psfgen) ERROR! Failed to parse autogenerate statement. Line 92: AUTO
> ANGLES DIHE PATCH
>
> psfgen) cross-term entries present in topology definitions
>
>
>
>
>
> --
>

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