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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 05 2018 - 11:18:56 CST

This might be an omission in the force field? It's possible that no one has
ever tried a terminal D-ALA before. Just glancing through the str file it
appears that CTD1 is just a drop in replacement for CT1 so that the CMAP
terms are correct. You can probably infer the missing parameters by using
the CT1 definition.

I would send this question to the MacKerell lab.

Brian

On Mon, Nov 5, 2018 at 11:07 AM Travis Hesketh <travis.hesketh_at_strath.ac.uk>
wrote:

> Hi all,
>
> I am fairly new to NAMD, so this could possibly be due to a mistake on my
> part, but I am running into the following error when trying to simulate
> proteins with D-amino acids mid sequence using NAMD 2.12 (also occurs in
> 2.13b2) and CHARMm 36 (the latest version, toppar_c36_jul18.tgz<
> http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul18.tgz>
> from http://mackerell.umaryland.edu/charmm_ff.shtml#charmm):
>
> FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CTD1 C NH1 CT1
>
> I put together some small tripeptide examples to test what was happening.
> The error occurs with AdAA and dAdAA. It does not occur with AdAdA, dAAA,
> dAAdA or dAdAdA. In other words, D-amino acids must be mid sequence (not at
> the N-terminus) and followed by an L-amino acid.
>
> The dihedral CTD1 C NH1 CT1 refers to atoms 15, 21, 26 and 28 in the first
> two cases, which are the following lines from the AdAA PDB file:
> ATOM 15 CA DALA 2 0.015 0.904 -0.100 1.00 0.00 A
> ATOM 21 C DALA 2 1.063 -0.122 -0.200 1.00 0.00 A
> ATOM 26 N ALA 3 2.418 0.231 -0.100 1.00 0.00 A
> ATOM 28 CA ALA 3 3.510 -0.715 -0.200 1.00 0.00 A
>
> The parameter files are loaded in the following order:
> parameters /users/travis/.charmm/par_all36_prot.prm
> parameters /users/travis/.charmm/par_all36_carb.prm
> parameters /users/travis/.charmm/par_all36_lipid.prm
> parameters /users/travis/.charmm/par_all35_ethers.prm
> parameters /users/travis/.charmm/par_all36_na.prm
> parameters /users/travis/.charmm/par_all36_cgenff.prm
> parameters /users/travis/.charmm/toppar_water_ions_namd.str
> parameters /users/travis/.charmm/toppar_all36_prot_c36_d_aminoacids.str
>
> The conf file, full log and the unsolvated PDB and PSF files can be found
> in the following pastes:
> https://pastebin.com/j7f8uxyJ - conf file
> https://pastebin.com/qf4gcYcz - log file
> https://pastebin.com/DZ7EaWN3 - pdb
> https://pastebin.com/HxP4qkSe - psf
>
> The PSF and PDB files were generated using psfgen, top_all36_prot.rtf and
> toppar_all36_prot_c36_d_aminoacids.str.
>
> toppar_all36_prot_c36_d_aminoacids.str was modified to remove the CHARMm
> commands at the beginning of the file, noted below, but is otherwise as
> supplied:
> set nat ?NATC
> set app
> if "@NAT" ne "?NATC" if @nat ne 0 set app append
>
> When researching the error message, I couldn’t find any NAMD-specific
> complaints, but there was mention of a similar error being encountered in
> GROMACS, though there didn’t appear to be a solution:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119045.html
>
> If anyone could shed any light on this, it would be much appreciated.
>
> Kind Regards,
> Travis Hesketh
> PhD student
> University of Strathclyde
>
>

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