Hi Sven,
This is a bug in Paramfit's dihedral parameter parser. It does care about
the order dihedrals are listed in the prmtop. As you have seen when
conducting a multiple molecule fit where the dihedrals happen to be listed
differently it fails to parse. I will fix this bug and send you a patch
ASAP.
You're correct that the order in which atoms are listed in a dihedral term
shouldn't matter: A-B-C-D applies to that dihedral as well as D-C-B-A.
Best,
Robin
On Tue, Nov 22, 2016 at 3:59 PM, Sven Hackbusch <s_hackbusch.u.pacific.edu>
wrote:
> Dear Amber Developers and Users,
>
> I am attempting to use paramfit from AmberTool12 to fit some dihedral
> parameters missing from the GLYCAM forcefield.
> I am using two small molecules (methylmethoxyacetate and methyl
> tetrahydropyran-2-carboxylate) to fit terms for Os-Cg-C -O and Os-C -Cg-Os.
>
> As the paramfit tutorial mentions, directionality of the dihedral terms
> should be irrelevant (i.e. Os-Cg-C -O should be the same as O -C -Cg-Os),
> but that does not appear to be the case:
> When I run paramfit with the parameter file generated from one of the two
> molecules, I get the following error in the output file:
>
> Reading prmtop file list: prmtops_list
> Reading prmtop file : methylmethoxyacetate.prmtop
> Reading prmtop file : methylTHP2carboxylate.prmtop
> No match for dihedral O -C -Cg-Os term 0 in prmtop!
>
> This would indicate to me that order does matter afterall. Additionally,
> when I generate the parameter file from the two molecules, the dihedral
> terms are not in the same order:
>
> methylmethoxyacetate:
>
> #V2 AUTO-GENERATED PARAMETER FILE - DO NOT MODIFY
> #
> # BOND INFORMATION:
> #### BOND REQ KR ####
> #
> # ANGLE PARAMETERS:
> #### ANGLE KT THEQ ####
> #
> # DIHEDRAL PARAMETERS:
> #### DIHEDRAL TERM KP NP PHASE ####
> O C Cg Os 0 1 1 1
> O C Cg Os 1 1 1 1
> O C Cg Os 2 1 1 1
> Os C Cg Os 0 1 1 1
>
> methyl tetrahydropyran-2-carboxylate:
>
> #V2 AUTO-GENERATED PARAMETER FILE - DO NOT MODIFY
> #
> # BOND INFORMATION:
> #### BOND REQ KR ####
> #
> # ANGLE PARAMETERS:
> #### ANGLE KT THEQ ####
> #
> # DIHEDRAL PARAMETERS:
> #### DIHEDRAL TERM KP NP PHASE ####
> Os Cg C Os 0 1 1 1
> Os Cg C O 0 1 1 1
> Os Cg C O 1 1 1 1
> Os Cg C O 2 1 1 1
>
> It is not clear to me at which point the terms are defined or how to change
> their order, so I am hoping someone can point me to a solution to my
> problem - possibly this is a mistake I made in generating the prmtop files?
>
> Thank you very much for your help!
>
> -Sven
> --
>
> Sven Hackbusch
> PhD Candidate
> Department of Chemistry
> University of the Pacific
>
> <https://www.linkedin.com/pub/sven-hackbusch/53/639/aa8>
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Received on Mon Nov 28 2016 - 16:00:03 PST
