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

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Nov 05 2018 - 13:13:06 CST

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--00000000000005710c0579efaf24--

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