VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Apr 24 2018 - 10:59:35 CDT

Basically psfgen shouldn't throw an error when it encounters "PATCH" in the default behavior it sees in a standard CHARMM .top file. Right now, in CHARMM, angles and dihedrals can be automatically regenerated after a patch is applied if that flag is present in the .top file. psfgen doesn't recognize it, and instead psfgen expects a "regenerate angles dihedrals" command after patches have been applied.

-Josh

On 2018-04-24 06:39:23-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

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<mailto: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<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fasharjm_at_gmail.com&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C3647d59166b8457e92ba08d5a9e06574%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636601703620843164&sdata=JnegKSZhVNQpfGFx1NjWMrG7l%2FNHbykrilBGr8mwmCM%3D&reserved=0>)
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

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Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto: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<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.charmm.org&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C3647d59166b8457e92ba08d5a9e06574%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636601703620843164&sdata=LONZKUf4DvwP4KyxSr%2Flq6hPNSGIwTEeDKoSpZpWvvE%3D&reserved=0>
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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