Re: Psfgen - bonding terms involving disulfide bridges

From: Reza (resal81_at_gmail.com)
Date: Fri Oct 04 2013 - 09:32:46 CDT

Thanks for the clarification!

Best,
Reza

On Oct 4, 2013, at 7:55 AM, Jrme Hnin <jerome.henin_at_ibpc.fr> wrote:

> Hi Reza,
>
> Most probably, the BPTI example is just old, and wasn't updated to reflect the change from C27 to C3* topology files, where all "generic" angles and dihedrals were removed from PRES entries.
>
> http://www.ks.uiuc.edu/Research/namd/wiki/?Namd27b1Release
> http://code.google.com/p/charmming/source/browse/trunk/head/charmming-private/toppar/toppar_all.history?r=487#578
>
> Ever since then, the "regenerate angles dihedrals" command has been necessary after applying patches.
>
> Cheers,
> Jerome
>
>
> ----- Original Message -----
>> Hi all,
>>
>> I followed the BPTI example in the psfgen manual
>> (http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf) and noticed that
>> when patching the disulfide bridges, the angle and dihedral terms that
>> involve the bridges are not automatically generated (e.g. SG-SG-CB angle).
>> This is also the case with AutoPSF.
>>
>> I found out that using the "regenerate" command after DISU patches seems to
>> generate the missing angles and dihedral correctly. So I'm just wondering if
>> the regenerate command is missing from the BPTI example or if it is
>> intentionally left out?
>>
>>
>> Thanks,
>> Reza

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