Re: 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 - 11:23:47 CDT

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>
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 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>
> 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)
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C3647d59166b8457e92ba08d5a9e06574%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636601703620843164&sdata=o7OAMgmnLiFMo3I%2B%2BsToVf6BPm6ZlItXUTogcNQvNtI%3D&reserved=0>
>>
>> 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
>> <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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