From: Lennart Nilsson (Lennart.Nilsson_at_ki.se)
Date: Tue Apr 24 2018 - 12:45:26 CDT
In recent CHARMM versions this is under user-control, and the default is to automatically generate angles/dihedrals after a patch command. It is never deferred to the writing of the PSF, which is not a required step - you can just generate and patch your PSF and then run your simulation/minimization/... without ever writing the PSF to disk.
Lennart Nilsson
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Vermaas, Joshua
Sent: den 24 april 2018 19:08
To: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>; brian.radak_at_gmail.com
Cc: vmd-l_at_ks.uiuc.edu; bishop_at_latech.edu; namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available
Yes. I think the way it is implemented in CHARMM is that angles and dihedrals are automatically regenerated after every patch command, or perhaps are deferred until writing the psf rather than immediately after segment generation.
-Josh
On 2018-04-24 10:23:51-06:00 Brian Radak wrote:
Oh I think I see now. This line isn't within a residue or patch definition, it's in the RTF "header". I'm still not clear what this is supposed to mean, though. Is it to indicate that the "first", "last", and "patch" commands should be understood to imply the coda "regenerate angles dihedrals"?
I think the best we can implement in psfgen is that these commands are ignored, much like the CHARMM NONBOND commands. In fact, it's not really clear that psfgen would do anything useful with that command even if it were correctly parsed (why would it regenerate while loading topology definitions?).
On Tue, Apr 24, 2018 at 11:59 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
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<mailto: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
*************************************************** SESSION DUMP **************************
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
psfgen) cross-term entries present in topology definitions
This archive was generated by hypermail 2.1.6
: Mon Dec 31 2018 - 23:21:02 CST
Info) http://www.ks.uiuc.edu/Research/vmd/
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) >>>>> 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
--