Re: [AMBER] saveamberparm in xleap does not recognize atom type F

From: Genzo Tanaka <gmastanaka.msn.com>
Date: Mon, 16 Apr 2012 12:13:13 -0400

Hello,
We built the CHN0 unit in Xleap and some of its force field parameters were provided through our lingwang.dat file. The atom type "F" in parm10.dat was not recognized when saving the topology file.
The last part of the log file was copied below, thought I have attached the edited version of the log file.
Unit Editor: > check CHN0Unit Editor: Checking 'CHN0'....Unit Editor: Warning: Close contact of 0.629348 angstroms between .R<CHN0 1>.A<H12 12> and .R<CHN0 1>.A<H34 34>Unit Editor: Checking parameters for unit 'CHN0'.Unit Editor: Checking for bond parameters.Unit Editor: Checking for angle parameters.Unit Editor: check: Warnings: 1Unit Editor: Unit is OK.> saveOFF CHN0 CHN0.libSaving CHN0.Building topology.Building atom parameters.> saveamberparm CHN0 CHN0.top CHN0.crdChecking Unit.Building topology.Building atom parameters.For atom: .R<CHN0 1>.A<F23 23> Could not find type: FFor atom: .R<CHN0 1>.A<F24 24> Could not find type: FFor atom: .R<CHN0 1>.A<F25 25> Could not find type: FParameter file was not saved.
Thanks,
Genzo

> Date: Fri, 13 Apr 2012 23:22:43 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] saveamberparm in xleap does not recognize atom type F
>
> On Fri, Apr 13, 2012, Genzo Tanaka wrote:
>
> > We worked on xleap in AmberTools 12.
> > Atom type F was not recognized when the command > saveamberparm CHN0 CHN0.top CHN0.crd
>
> It would be *very* helpful to give the exact error message you received.
>
> > However, > saveOFF CHN0 CHN0.lib
> > correctly saved all atom types.
> > parm10.dat was loaded in xleap, and atom type F was included.
>
> What you see is expected behavior. Saving an off file does not check to
> see if parmeters are available for all the types of bonds you have in
> the molecule. Having missing parameters only shows up when you execute
> "saveamberparm". You will probably need to create a frcmod file with the
> appropriate parameters in it. Since you don't say how you constructed the
> CHN0 unit in the first place (or what it is), it's hard to give any more
> specific advice.
>
> ....dac
>
>
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Received on Mon Apr 16 2012 - 09:30:03 PDT
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