Re: Distorted peptide bond with new residue

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Thu Jul 05 2018 - 17:39:25 CDT

I did not do that, I applied patches and generated the structure. How do
you do that?

On Thu, Jul 5, 2018, 6:05 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Ahh, that's a different problem. Did you regenerate angles and dihedrals
> after a patch? A mistake I've made more often than I'd care to admit is
> forgetting this after a patch, and as a result not having *any* bonded
> terms at the join point to keep the geometries sane.
>
> -Josh
>
>
>
> On 2018-07-05 16:00:39-06:00 Nick Palmer wrote:
>
> I will try the extra bonds term, however the bond is not just cis, the
> n-co-ca bond angle is 180 degrees by the end of the minimization.
>
> On Thu, Jul 5, 2018, 5:34 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
>> Hi Nick,
>>
>> The initial geometry probably has more to do with it. The dihdedral that
>> describes a peptide bond has the functional form cos(2*phi-180), which has
>> minima at 0 and 180. Normally, the initial geometry is such that you get
>> the correct trans peptide bond upon minimization, but in your case the
>> minimizer just found the cis-peptide potential energy minimum, which you'll
>> need to fix. VMD has a snazzy cis-peptide plugin (
>> http://www.ks.uiuc.edu/Research/vmd/plugins/cispeptide/
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fplugins%2Fcispeptide%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C43be3d95ce30446d6a4d08d5e2c2bda8%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636664248394423262&sdata=qCZhFr2%2FYRVEFvufgRzcNnrhUu%2BKCbQZyke1BFYk%2ByM%3D&reserved=0>)
>> that will let you fix this for normal amino acids, although I don't know if
>> the selections it uses under the hood will recognize your modified residue.
>> Another possibility is to add a ridiculous extra-bonds dihedral term in
>> addition to the regular bond to make the cis-well disappear (this is what
>> the plugin sets up for you). See
>> http://www.ks.uiuc.edu/Research/namd/2.12/ug/node27.html#SECTION00086400000000000000
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.12%2Fug%2Fnode27.html%23SECTION00086400000000000000&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C43be3d95ce30446d6a4d08d5e2c2bda8%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636664248394433267&sdata=8CvZWgHNPZIbSMReh0p20wOlsbtoK3Auay0gQjBsOBs%3D&reserved=0>
>>
>> -Josh
>>
>>
>>
>> On 2018-07-05 15:22:30-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>>
>> Hello everyone,
>> I have been trying to create a new residue topology and add parameters to
>> it. The topology and parameters work, however when minimizing the structure
>> the peptide bond connected to the c terminal of the new residue is
>> distorted so that the peptide bond has a 0 dihedral angle rather than the
>> 180 it is supposed to have. When creating the psf for this molecule, I had
>> to manually link this residue to the rest of the chain with a LINK patch--000000000000d1332905704838cd--

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