VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Mon Apr 23 2018 - 19:57:47 CDT

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@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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