Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36

From: Gumbart, James C (gumbart_at_physics.gatech.edu)
Date: Mon Nov 05 2018 - 14:17:46 CST

You should confirm, but aren’t all of the bonded parameters symmetric with respect to l- and d-amino acids? As long as the phase is 0 or 180, it shouldn’t matter (the CMAP is asymmetric though). Meaning you could just copy in the missing ones by hand.

Best,
JC

> On Nov 5, 2018, at 2:13 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> Hi Travis: my apologies, I didn't see that you were already using the
> stream file.
>
> Try emailing MacKerell's lab, but keep in mind also that some of the stream
> files are contributed by other groups, so you may be directed to the CHARMM
> forum anyway.
>
> Giacomo
>
> On Mon, Nov 5, 2018 at 1:55 PM Travis Hesketh <travis.hesketh_at_strath.ac.uk>
> wrote:
>
>> Hi Giacomo,
>>
>> Thank you for your quick response. I am already using the stream file
>> supplied with the CHARMm distribution (located in
>> toppar/stream/prot/toppar_all36_prot_c36_d_aminoacids.str). It appears to
>> contain L->D and D->D dihedral angles, but not D->L (which explains why
>> AdAdA will run, bur dAdAA will fail with the error). I outlined the missing
>> lines in my response to Brian, I will email the MacKerrel lab about the
>> issue.
>>
>> Kind Regards,
>> Travis
>>
>> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> Date: Monday, 5 November 2018 at 17:38
>> To: NAMD list <namd-l_at_ks.uiuc.edu>, Brian Radak <brian.radak_at_gmail.com>
>> Cc: Travis Hesketh <travis.hesketh_at_strath.ac.uk>
>> Subject: Re: namd-l: Error with D-amino acids mid-sequence using NAMD
>> 2.12/2.13b2 and CHARMm36
>>
>> Hi everyone, there is a stream file for D amino acids in the CHARMM
>> distribution, under stream/prot. This can be adapted for use with PSFGen

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