AMBER Archive (2009)

Subject: Re: [AMBER] sequence function

From: taufik.alsarraj_at_utoronto.ca
Date: Mon Apr 06 2009 - 12:06:50 CDT

sorry the typing error
> the function i use in xleap is >system = sequence {dna smcc sur}

Quoting taufik.alsarraj_at_utoronto.ca:

> Hello,
>
> I am trying to use the sequence function to connect a dna strand to a
> linker to a surface
>
> the function i use in xleap is >system = {dna smcc sur}
> all three components have head and tail atoms and there is a *.frcmod
> file that describes the parameters not in *leaprc.ff99SB and
> leaprc.gaff.
> Individually, dna, smcc and sur can run in sander, i tried connecting
> dna and smcc only and it works. However, connection all three or smcc
> and sur does not work. xleap crashes giving the following error
> message, i only attached the end of the error message
>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-O7-SI2-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-O2-SI1-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-O4-SI1-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-O227-SI90-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named H273 from Sur did not match !
> !
> !ABORTING.
>
>
> SI1 etc are atom names of an Si type, i am not sure why Add ATOM Types
> function is needed as these parameters are defined in my *.frcmod file.
>
> Many thanks,
> Taufik
>
>
>
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