Hi Robin,
Thank you very much. I will give this a try.
-Sven
On Tue, Dec 6, 2016 at 12:00 PM, <amber-request.ambermd.org> wrote:
>
> Date: Mon, 5 Dec 2016 16:56:00 -0800
> From: Robin Betz <robin.robinbetz.com>
> Subject: Re: [AMBER] Paramfit for multiple molecules
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAL9_cpdFH0mEX_EegsFs0sCpKWPO8uoc6gjgVXk6OHzp
> UYvFhA.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sven,
>
> I've fixed the bug. Please replace
> $AMBERHOME/AmberTools/src/paramfit/file_io.c with the attached file and
> recompile. I will include this as part of the next bugfix for AmberTools as
> well.
>
> Let me know if you have any other problems.
>
> Best,
> Robin
>
> On Mon, Nov 28, 2016 at 3:47 PM, Robin Betz <robin.robinbetz.com> wrote:
>
> > 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>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 Tue Dec 06 2016 - 14:00:03 PST
